The Appendix/Cave Fish Eyes/Etc. are (NOT) vestigial

I appreciate the engagement, Ashwin. My life is in a particularly busy spell and to do justice to your response would take more reading than I’m able to commit to right now. (I can’t even particularly justify taking the time to read the response I’m currently replying to… I haven’t read all those block quotes.) I think others have already adeptly addressed the main lines of your argumentation, though. I trust that their responses are sufficient, though I’m fairly sure you won’t find them convincing.

Grace and peace to you (truly) —
AMW

To what extent can we “refine” the theory of evolution? This theory seems to be like theseus’ ship!

From Darwin’s times, they have pretty much refined and replaced every component of the theory.The last standing component was common descent as represented by a universal treel of life.
Now scientists are saying the said “tree of life” does not exist. That this part of Darwin’s hypothesis has been falsified.

So we come back to my first question. What exactly is the theory of evolution? Is it a falsifiable theory or some kind of unfalsifiable worldview… a Ship of theseus that can have every component falsified and replaced but still claim to be the same old ship???

Draw the tree… compare it to Drawins hypothesis… place a creationists tree alongside it. If you were classifying types of trees… The current tree accepted by consensus would be classified along with that of creationists as an unrooted tree…

Think on it.

Genomic studies do not represent what happened to particular species… it doesn’t or atleast shouldn’t generate a species tree. Biologists have arrived at trees for decades by removing evidence that pointed to a non-tree reality at the biochemical level. Once they correct this bias, and repeat their studies, we will know what the real picture is.

Now you are just repeating a statement of faith. The papers point to a methodolical error in how people have been constructing trees. they have been ignoring the major part of the genetic information. 99% in case of universal tree of life!. let me quote from a paper on eukaryote origins -

Blockquote
How we think we should depict evolutionary history has, of course, an enormous effect on how we analyse data, how we write analytical software and how we depict the final results. If we feel that the evolutionary history of a dataset has been tree-like, then it is likely that the first, perhaps only, analyses we carry out will be a phylogenetic analysis using software that generates, as an output, a tree. We know of course that human populations do not have a tree-like history; therefore, we are usually disinclined to use software for tree reconstruction to depict these histories [2]. A phylogenetic tree can always be derived based on the complete genomes of two parents and their children. However, we know that the tree will be meaningless, because a tree-like process did not generate the data. What this means is that the outcome of an evolutionary analysis is always contingent on our a priori opinions for how the data have evolved. In some cases, as in the above example, our knowledge of the process that generated the data is good enough to let us unambiguously avoid the use of a particularly poorly fitting model (i.e. a tree) to describe the data (i.e. the relationships between the genomes of two parents and their progeny). However, in most cases, we lack the knowledge to unambiguously reject a model (or a class of models) based on previous observations. In such cases, a better course of action would be to consider a variety of models and ask which fits the data best (if not adequately).

For now we can say that. But since all our conclusions are based on analyses that assumed trees, we cannot be sure whether it actually is what the data* says… Its an interpretation forced by an a priori assumption.Maybe the interpretation is true and agrees with the data… maybe not…
However, even of higher phyla show tree like patterns, what you will get is an unrooted tree…Like creationists draw. Not the kind predicted by the modern synthesis.
An unrooted tree is closer to what someone like Behe, or any creationist (or someone like shapiro) would predict rather than what the modern synthesis does.
Its probable that early eukaryotes also do not really show any tree-like organisation (see paper below).
The paper describes the eukaryotes not arising from any particular group (i.e archaebacteria and eubacteria), but rather as a mix and match between the two from some kind of “symbiotic” event. i.e its something of a chimera. (not descent via modification).
http://rstb.royalsocietypublishing.org/content/370/1678/20140323

In short, what we have is not common descent. What we have is two or possibly three unrooted trees.
And the fact that the analysis of all trees we have is based on a biased interpretation of data.

I will come to it when i have time (mainly because i am curious). I have put it on the back burner because its will not prove anything. if it turns out to be diversity in species or kinds… you will still claim its vestigial.
Even if it turns out to be vestigial, it will still not make any difference. because, i have already accepted in principle that some ammount of adaptation does happen. (Even YEC’s accept that). It seems to be an excercise in futility and perhaps a never ending chain.

I accept that the authors do not question the tree like nature of animal classification. I have noted in one of my posts that their main area of expertise/work is not animal classification. I will come to animal classification later on.The main points i wish to make from the papers are as below -

  1. The so called tree of life is unrooted… i.e it does not end ins LUCA. It is actually three separate trees… (as of now)… and perhaps more appropriately 3 separate networks of genetic relationships which do not necessarily show descent.
  2. Observations of a tree like appearance can be because of assumptions of a tree.
    Would you agree to the same?
  3. The authors make a case that looking for tree in Biological data is a wrong method and can influence programs to give skewed data. hence they propose that Scientists should look for networks of relationships to get unbiased data from which to draw conclusions.

Some people have carried forward such a research programe… And perhaps it will turn out that genomes of animals show a nested heirarchy… perhaps not. That is yet to be determined through empirical science.Though i would expect to find trees at some point… either among animals… or mammals… or atleast families… (But how would that differ from my Automobiles example??)
Below is an interesting study within mammals.

Blockquote
With the advent of more genome data becoming available, along with the ability to explore deep divergences in greater detail, it is becoming evident that evolutionary processes are best interpreted as networks. Networks naturally highlight the conflict and difficulties of previous phylogenetic studies to find a congruent bifurcating tree within this group. The hope of phylogeneticists that whole genome data would one day yield a single, stable and bifurcating evolutionary tree [18], [63], [64], is not fulfilled for some parts of the placental mammalian tree. However, it seems that a more valuable lesson can be learned from genome analyses. That is, some divergences are not characterized by bifurcations but rather that the evolution of some placental mammals represent a complex pattern of genealogies of different parts of the genome. Speciation processes that can be revealed from genome data even for deep divergences, define this pattern. The evolution of Carnivora, Perissodactyla, Chiroptera, and Cetartiodactyla (Laurasiatheria) represent such a case.

The bare minimum we can conclude from the paper is that Genome studies do not support a bifurcating tree of life for Laurasiatherian mammals. The data better supports a network.
A tree has to be force fitted.
I dont expect network analysis to be very popular when studying animals… because we human beings think more easily in terms of nested heirarchies.
So give it a decade or two to catch on…

Think… what exactly is an “interspecies gene transfer”?
Bapteste is quite clear… he emphatically says that Darwins hypothesis of the tree of life has been falsified… Can he be any more clear???
I gave extensive quotes to avoid being accused of “quote mining”… so that the context is clear. let me just quote the relevant part as you have requested -

Blockquote
Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.

Note: Bapteste who woeks mainly on prokaryotes is emphatic that prokaryotes dont fall into a tree pattern. He believes animals do…
However, that may not be the case. as suggested by a paper i have referred to above…
Even if animals do fall into trees, we have unrooted trees lwhich is closer to a creationist expectation that Darwin’s.

Sorry if i gave the wrong impression… I don’t believe you intend to deceive any one.My impression is that you are genuinely sincere.
However its possible for anyone of us to fall for strategies in discussions which are inherently deceptive…

I replied to @T_aquaticus on a similar question he raised about animal falling into tree like structure. The answer is the same.

It was good talking to you… I hope you gained something from the interaction.
As to the responses i get, if i ma not convinced, i give the reason why.

God bless.
@AMWolfe

And yet … you call one of the BioLogos Mission Statements as deceptive - - when in fact it goes to great lengths to avoid any deception! To paraphrase:

o Evolution on Earth requires God;
o Any model of Evolution of that excludes God’s participation is rejected;
o Evolution must include a teleological role for God.

So, what you are saying is that your own position is also deceptive? If it isn’t, how exactly do your positions differ from the positions set out by BioLogos?

Given that you don’t accept the refined theory, does it really matter?

The one mechanism that Darwin put forward was natural selection, and it is still a central pillar of the theory.

“To be sure, much of evolution has been tree-like and is captured in hierarchical classifications. Although plant speciation is often effected by reticulation (80) and radical primary and secondary symbioses lie at the base of the eukaryotes and several groups within them (81, 82), it would be perverse to claim that Darwin’s TOL hypothesis has been falsified for animals (the taxon to which he primarily addressed himself) or that it is not an appropriate model for many taxa at many levels of analysis. Birds are not bees, and animals are not plants.”
Doolittle and Bapteste, 2007

Want to try that one again?

What creationists are claiming that all eukaryotes share a common ancestor and evolved from that common ancestor?

The tree is real for very large groups of species, such as the eukaryotes. Do you accept common ancestry for all eukaryotes? If not, then why make the argument you are trying to make?

The tree for animals has already been determined empirically, as the authors of the papers you are quoting have already pointed out.

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Hi Ashwin,

It seems to me that you are willing to agree with the biologists that descent with modification explains from the scientific perspective how the primates are descended from a common ancestral population, and that descent with modification, be it structured as a tree or as a network, explains from a scientific perspective the origin of species both small and large. You do have serious reservations about origin-of-life pronouncements, and think that the first cellular organism was the result of God’s direct intervention–i.e., a miracle–rather than through regular scientifically tractable means. You also believe that any tree that biologists can reconstruct will only reach back to the origin of multi-cellular life some 630 MYA.

If I have understood you correctly, we are largely in agreement on these points. The only substantial difference I see between us is that I am open to the possibility OOL researchers may be able, someday far in the future, to infer a scientifically tractable mechanism through which biological life on earth came to exist. Should that day arrive, I would regard the mechanism as an exhibition of God’s marvelous creativity and design. For today, however, I would agree that the RNA world is a hypothesis rather than a theory.

One of the most recent sources you cited in another thread reached this conclusion:

I agree with this conclusion that Marvin quoted. If you are willing to agree with that conclusion, too, then we can throw a party, hand out trophies, and move on to other pursuits.

Grace and peace,
Chris

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So do you agree with the authors?

“We exemplify this on a subset of 1159 suitable genes that have individual histories, most likely due to incomplete lineage sorting or introgression, processes that can make the genealogy of mammalian genomes complex.”

It’s not as if some of the genes they looked at demonstrated more relatedness to jellyfish or amphibians for some mammal species. All of the genes they looked at put these species well within the mammal clade. The only arguments they are putting forward is for the fine details of that tree, and the noise within that tree caused by very real biological processes like incomplete lineage sorting. It is an argument about noise being high when looking at the deep nodes of a tree WHICH IS EXPECTED WITH EVOLUTION. You might as well claim that a blurry photo of a distant galaxy means that galaxies don’t exist.

“To be sure, much of evolution has been tree-like and is captured in hierarchical classifications. Although plant speciation is often effected by reticulation (80) and radical primary and secondary symbioses lie at the base of the eukaryotes and several groups within them (81, 82), it would be perverse to claim that Darwin’s TOL hypothesis has been falsified for animals (the taxon to which he primarily addressed himself) or that it is not an appropriate model for many taxa at many levels of analysis. Birds are not bees, and animals are not plants.”
Doolittle and Bapteste, 2007

Can he be more clear?

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Hi Ashwin,

You are basing your conclusions on a 2011 paper. However, later research that used a much larger dataset strongly refuted the conclusions of that paper. The 2017 paper is:

Chen, et al. Phylogenomic Resolution of the Phylogeny of Laurasiatherian Mammals: Exploring Phylogenetic Signals within Coding and Noncoding Sequences.

Here is the tree that is strongly supported by their analysis:

Laurasiatherian_tree

I refer you to the paper for the mathematical details.

Grace and peace,
Chris Falter

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Which means Biologos rejects the Scientific theory of evolution which is a theory that excludes Gods participation and excludes a teleological role for God.

My position is not deceptive because i don’t use the term evolution to describe a belief that is patently not Evolution and in fact denies evolution is ultimately a natural process.

Yes it does. It shows whether the so called “theory” is falsifiable … and what exactly the theory itself is. For example, if evolution as a theory can be refined ad infitum and all its components replced at some point or the other, its not a falsifiable theory. Its an over arching philosophy which is essentially untestable.
I hold that the idea of evolution is unfalsifiable… and every component which can be falsified has been falsified.

Ever heard of the neutral theory of evolution? Natural selection has been cut down to size. It is not what Darwin claimed it would be… i.e a unifying principle. Its valid in some cases/example of evolution and invalid in others…
Its also untestable/unfalsifiable… Biologists are even now looking for a definition of Natural selection that would permit falsification.

Yes… the point being that Tree of Life is Falsified… At best… its a “Tree of animals”…
not even plants and animals. Reticulated evolution is another word for data that is not tree like… it refers to a network.
You have lost Prokaryotes, eukaryotes and plants…
Even creationists wouldnt have a problem with the last comment :slight_smile:
** Birds are not bees, and animals are not plants.”**

Even Biologist are not claiming eukaryotes have a common ancestor… The current understanding is that eukaryotes are a hybrid of Eubacteria and archebacteria traits/genes… also cyanobacteria contribute to plants at some level too…
I dont think anyone even claims the first hybrid gave rise all the families of eukaryotes… thats also a reticulated mess and scientists are trying very hard to fit it into a tree…
Why would creationists make such a claim when even evolutionary biologists hesistate to?
My point is that Biologists are now beginning to repesent life as creationists wouls… as a unrooted network on an overall level with trees found among more similar organisms.

No the idea is, life is not a tree… its a network of gene sharing.

Are you claiming that common ancestry started only with eukaryotes?
And if most unicellular eukaryotes turn out not to show tree like patterns (which is a highly likey scenario considering the various conflicting results with respect to where the eukaryote Ca is positioned in the tree), would you claim common ancestry started out only with multicellular organisms? And what do you do when plants show extensive reticulation (as they are shown to do)?

Yet they somehow feel compelled to propose a network type of relationship… reticulated networks are currently being used to show the relationship between birds also for your information… Basically we have a broken chain of several tree like patterns. this is not the unbroken chain of descent predicted by Common ancestry.

I was pointing out where science stands currently in my view.I am currenlty agnostic on primate evolution.I am not philosophically commited to any from of scientism as it stands on a false belief in the inerrance of scientific consensus.Let me give an example. In Einsteins times, it was the opinion of most scientists including Einstein that the universe was eternal, and went through and endless cycle of expansion and collapse. If any one changed their theology based on Einsteins then scientifically valid view, they would have been in great error.Though i do read science, i am very careful about what i believe is truth with a capital T. I allow philosophy and world views (including views on the bible) to educate my final beliefs and i would expect this from any rational person.
I prefer a wait and watch policy with respect to scientific consensus. My theological views are formed in the traditional way. reading the bible and praying.
I expect the next few decades to show the following based on my understanding of the issues-

  1. That natural genetic engineering is responsible for novelty/and big changes in phenotypes/morphology.(LGT, endo-Symbiosis, Hybridisation, and other yet to e defined processes that achieve phenotypic change through inserting pre-defined genetic content into a host genome).
  2. As knowledge of complete genomes increase, i expect reticulated networks to emerge as a better representation of the relationships among species even in more complex domains such as the animal kingdom.
  3. That someone would redefine evolution to mean “Descent with modification”, where said modification is not restricted to causes related to lineage or something along those lines…
  4. Textbooks will be updated decades after the fact with new just so stories…

There is a big need for a paradigm shift in biology…

Its possible to arrive at a statistical tree of life (i.e a tree of trees) and also a tree of life from single genes. I don’t dispute that. However, there is no reason why one set of genes should tell a different story from the other if both are inherited from a CA. Its the overall picture that is reticulated… I dont think the 2011 paper disputes that Trees of life can be created…
They just tell different stories based on the genes you select. Introns tell different stories… coding sequences tell another story… micro Rna based comparisons tell something else.
If the introns are inherited from a CA, then where do the CDS and other gene sequences which tell a different story come from?
This is why Scientists like Baptiste say that these genomic trees need not really represent the history of a species vis a vis its lineage.Its just a way to classify or represent organisms.

@Ashwin_s,

Didn’t we cover this already? BioLogos says it rejects the science of Evolution when defined in a way that excludes God.

Is there more than one person using your @Ashwin_s login? That might explain your inability to maintain continuity in your discussions.

Is there a way in which the science of evolution is defined in a way that includes a theistic God?
It’s defined excluding God as a possibility.

If the theory wasn’t falsifiable then it wouldn’t be refined. The theory changes because parts of it are found to be wrong, and we know that parts of the theory are wrong because IT IS FALSIFIABLE.

Here are 29+ potential falsifications for the theory of evolution:

That’s like saying the idea of erosion has been falsified in geology because there are places on Earth where there is deposition taking place. Natural selection, both positive and negative, still occur in all genomes as well as neutral drift. Finding sections of a genome where junk DNA is accumulating neutral changes does not falsify the claim that sections of the genome are under purifying selection.

You reject the tree of animals, which is the whole point. You don’t accept the evidence that animals descended from a common ancestor through vertical inheritance.

And creationists accept that all eukaryotes, from protists to humans, evolved from the common ancestral pool of eukaryotes that were the result of this hybridization, just as almost all scientists do?

Do you or do you not accept that even all primates share a common ancestor? yes or no?

And what are the mechanisms they propose for the cause of this network?

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If you define the actions of God as those which go against natural processes then you will probably end up disproving the existence of God as more evidence accumulates for natural processes.

That is completely false. Science doesn’t exclude any possibility. Science can only include possibilities that are supported by evidence.

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No, it’s not. The science of evolution is completely agnostic on the subject of God. Unless you think describing the natural mechanisms underlying a process is the same as saying that nothing but those natural mechanisms can possibly exist.

It’s like saying, when I pray I make physical sound which travels x distance and I definitely don’t see any evidence of God in that range, so praying is pointless. (Disclaimer: I don’t think praying is pointless.) You could probably even design a test to figure out if the sound is being fully absorbed by the expected physical materials in x range, and then get even fancier and repeat it all for the electromagnetic signal of your brainwaves.

Would you honestly expect any of that to tell you anything about the existence of God?

So then why would you insist that if the science of evolution isn’t affirming God, it’s “by definition” excluding God?

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The theory of gravity neither includes nor excludes God.
The theory of quantum mechanics (which has a prominent role for randomness) neither includes nor excludes God.
Meteorology (which has a prominent role for randomness) neither includes nor excludes God.
The theory of evolution neither includes nor excludes God.

Grace and peace,
Chris

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Since only parts can be falsified. It leaves a core that cannot be falsified.
Common ancestry has been falsified in some cases… and I guess is being refined.However, the refined version seems more general that the original one.
Hereditary change through mutations is being added to by processes such as endosymbiosis, HGTs,ERVs,Gene duplication etc.
So what is the unfalsifiable core. Why retain the name evolution for the new extension? Or has the idea of evolution become so general that it is just a different name for “natural causes”?
If the unfalsifiable core is naturalism, it’s a philosophy. Not a scientific theory.

Ideas cannot be falsified perse. However, if there was a theory that a particular feature in nature is caused by erosion, it can be falsified. Darwins theory is that Natural selection is the creative force behind all the variation we see causing random variations to accumulate in a directional manner and thus shape all the design features observed. That idea has proven to be false.
I accept its very difficult to falsify natural selection as it is not defined well enough to be falsified.

Its a fair question. And the answer is that scientist have consistently said so.

Blockquote
It was Darwin’s greatest accomplishment to show that the complex organization and functionality of living beings can be explained as the result of a natural process—natural selection—without any need to resort to a Creator or other external agent. The origin and adaptations of organisms in their profusion and wondrous variations were thus brought into the realm of science.

i.e, God is not needed as an explanation.

Blockquote
Natural selection sorting out spontaneously arising mutations is a creative process because it causes favorable mutations to combine and accumulate, yielding a great diversity of organisms over eons of time. But there are important features that distinguish the kind of “design” achieved by natural selection, namely the adaptations of organisms, from the kind of design produced by an intelligent designer, an engineer.

i.e The work of natural selection will be different from that of a creator God. Here the scientist is claiming that they can differentiate whether a “design” is made by God or not. They make logical arguments against a designer by trying to show that the “designs” could not have originated from anyones mind.
I have heard christians like @Bill_II in this forum repeat this same argument and suggest that the design is not intelligent… i.e the Designer is dum (either in that he designed wrong or used bad tools)

Blockquote
This is Darwin’s fundamental discovery, that there is a process that is creative although not conscious. And this is the conceptual revolution that Darwin completed: the idea that the design of living organisms can be accounted for as the result of natural processes governed by natural laws. This is nothing if not a fundamental vision that has forever changed how mankind perceives itself and its place in the universe.
http://www.pnas.org/content/104/suppl_1/8567#sec-8

What people like @gbrooks9 describe is not evolution in any shape or form as taught by someone like Ayala and most other scientists. It is different in the following points -

  1. @gbrooks says there is ultimately a designer. Evolution emphatically says the designer is natural selection and you can tell by looking at the design. If God used truly “random”, undirectional process in designing organisms, he is not interested in the details and so the design does not reflect Gods genius… but rather natures mindlessness. (as per evolution).
  2. @gbrooks9 says the process needs God to be a coherent explanation. Evolution claims the process does not need God to be a coherent explanation.
  3. @gbrooks9 claims a conscious being, i.e God is ultimately behind evolution, while scientist are clear no conscious being is involved.

Now, we could nitpick on the difference between philosophical materialism and methodological materialism, but this so called difference is absolutely lost in how scientists interpret, present and teach evolution to each other or the general public. Most of these scientists are moved by a fundamental vision.
Its a difference that exists only in the minds of Theistic evolutionists.
@Chris_Falter: we discussed similar stuff.

All the parts can be falsified, as already demonstrated.

Why wouldn’t it be added? That is how nature works, so it is part of the theory.

Evolution is the theory of how organisms change over time. If HGT, ERVs, gene duplications, and the like are evidenced mechanisms that cause change in species over time, then they should be included as part of that theory.

Evolution isn’t a religion. There are no tenets of Evolution that need to be dogmatically defended and held on to. What the evidence shows is what the theory is. Period.

The theory of evolution is the same as every other single theory in science. If you object to the theory of evolution citing natural mechanisms, then you are rejecting the whole of science and the scientific method.

The theory is that the vast bulk of the genomes of animals was inherited through vertical inheritance, and that the differences between species are due to genetic changes that were blind to the fitness of the organism. Those genetic changes were then filtered through natural selection and neutral drift.

All of these parts of the theory are exceedingly testable and falsifiable. Numerous and massive departures from a nested hierarchy would falsify vertical inheritance. Lack of sequence conservation in functional DNA would falsify selection and neutral drift. The pattern of transversions and transitions throughout the genome would falsify the theory that mutagenesis is blind to fitness. All of this is so easily testable.

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It wasn’t a discussion at all. You had made the same assertion about the theory of evolution excluding any possibility of God for the n-th time. In response I raised several points about other disciplines of science that use similar methodologies (incorporating randomness) and are often used by atheist apologists.

You clicked the reply button and typed some words. Your words essentially repeated your assertion without addressing any of the points I had made.

I don’t know what our interaction should be called. But I wouldn’t call it a discussion.

Grace and peace,
Chris Falter

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I also feel you didn’t get my point.
If that’s what you mean.

Can provide a formal statement to this effect from any source? I would be particularly interested in what is meant by “a vast bulk”… is that a number… an opinion… or an assumption?
When you say genetic changes were blind to fitness… what exactly do you mean? What about epigenetics?.

It’s been falsified extensively in single celled organisms… we have already discussed that…

Functional DNA is defined based on sequence conservation… B that count 8.2% of the human genome would be functional… and your claim would be circular reasoning.
As per ENCODE 80% has some biochemical function… if that is true it would falsify you claim…
So your choice is between circular reasoning and falsification.

I don’t object to natural mechanisms. I object to generalising the theory through refinements and tautologies to the extent that it is the same as saying “change happened through natural means”.

So what exactly is the theory?
Is it “genetic change happens through natural processes”?

All the claims have been falsified.