Farina vs Stephen Meyer

Just to note upfront this is MUCH longer in scope, so I will split the discussion of the video itself into multiple posts because I don't know if I have one good block of time to get it done.

Consider this "Part I" of the analysis. I'll post the same Farina video set at the correct time stamp to make things easier to follow. 

PLEASE DO NOT talk about general DI, ID stuff here. Or general stuff about Farina or Materialists. There's another thread for that, this specific thread is simply about the following video and the references it makes along with any rebuttals to the claims Farina makes. Thanks!



The first part of this is about the Wedge Document, where it seems Farina is saying the outright statement towards an agenda is proof that the DI is not doing actual science. Yet we have numerous instances of STEM academia censoring and deplatforming views that would challenge the Materialist faith.

Farina also claims that a lot of great things about Western civilization were only possibly when the grip of religion was loosened and so religion has no credit in varied positive aspects of Western thought. He also strongly suggests Materialism is just a buzzword and that Materialism hasn't had many or any negative effects on society.

Those are really broad claims, but I will try to get into them. I think both sides are ignoring the historical reality, to some degree and refusing to acknowledge the other side is partially right. Did the weakening of the Church allow for Enlightenment values? I don't doubt it, but at the same time a lot of religious though[t] did furnish how people thought about the world, and whether it was intelligible to mortals. Similarly a lot of Materialist thinking of people as commodities was challenged by Christian values at times -- see religious inspiration for global Abolition...which isn't to say there weren't pro-slavery Christians and anti-slavery Atheists who may have been Materialists...

Any way, examining the history of the West if not the world will require subsequent posts so let's move on for now.

Farina then notes a large amount of funding for the DI does come from Christian Fundamentalists who do want a theocracy. This I do think is a fair charge of possible bias, though it seems to me there are a variety of Materialist backed forces that also are biased. Big Pharma is not going to want you to believe in psychic healing, and the Anti-Depressant Scandal was more Materialist-based ideas about the mind being believed.

The next part i[s] about how Meyer uses books to get around peer review. I think this puts peer review into an unrealistic sacred light, as if Meyer would get a fair shake in any journal biased toward Materialism. However I do agree that, given there are even Christians who doubt ID, it is valid to ask whether the scientific arguments Meyer brings hold up. I would note that Brian Josephson is a Nobel Prize winning physicist and he highly regarded Signature in the Cell. IIRC the atheist philoospher Nagel also had some praise for the book.

Now getting to the core aspect of the scientific argument and Farina's rebuttal. Farina structures the ID argument as follows:

1. Evolution says there should be gradual change
2. We should see it.
3. We don't at all!
4. Evolution is false.

This is based on what Meyer says in this video:




(Note I'll summarize this video, then continue with the analysis of Farina's rebuttal after in future posts. Apologies, this is just too big to do in one sitting!)

Meyer says Darwinian evolution asserts two main propositions:

1) The history of Life can be thought of as a great branching tree, going back to a single celled common ancestor. This history is a gradual change from one simple ancestor to all life in the present.

2) This gradual change is driven by the mechanism of variation, which in modernity we call mutation due to errors in the sequencing of digital characters in the DNA. This process is also held by STEM academia by Dawrinists and Neo-Darwinists to be unselected without any Design influence.

Meyer then goes into how the fossil record actually challenges both points, arguing we don't see enough transition in the record. According to Meyer the majority, if not entirety, of what we see are variations within some particular set of forms and then new forms that don't seem to a mere variation of prior transitions.

He then gives some examples, such as the Cambrian Explosion and later the Great Ordovician Biodiversification Event. He also argues that appearances of the first insects, first reptiles, first flowers, and first mammals are examples of a sudden appearance of diversification that for him seems disconnected in major ways from what life came before. He notes Bechly wrote an article about 17 such explosions of new forms. (Will try to find this later)

Meyer notes that Darwin noted issues of ancestral forms, including the Cambrian Explosion. Darwin himself thought the issue was incomplete sampling - we haven't found all the fossils out there - AND/OR incomplete preservation - the forms were there but were not preserved.

Meyer claims the fossil record at present shows even more new forms in the Cambrian Explosion that need to be explained. Regarding incomplete preservation, Meyer notes there's shale in China where more Cambrian forms were found, beneath that level of shale they've found embryo's that have been fossilized. Meyer notes these are extremely small (sometimes microscopic) and extremely soft fossils, so why weren't the transitional forms found? (Will look this up later).

Meyer then goes on to say there are few transitional forms in narrow taxonomic groups, but not there for major morphological forms for which there's discontinuity.

Meyer then goes into population genetics, which he says allows us to calculate the "waiting time" for evolution to occur. He says this increasingly causes problems for RM + NS due to complex structures that require coordinated waiting times. He says the waiting times end up being far too long for what we see in the actual fossil record.

The video concludes by equating (in some sense) new forms in the taxonomy to new information. If we want computers to have new functionality we need to provide new code. So just as a programmer adds new code, Design is adding biological information.

That's the conclusion of this Meyer video, will then get into Farina's rebuttal in the next post.

The following is the same video as above, just set to the correct timestamp for convenience:

https://youtu.be/Akv0TZI985U?t=391

Recall Farina structures the ID argument as follows:

1. Evolution says there should be gradual change
2. We should see it.
3. We don't at all!
4. Evolution is false.

Farina claims that there are a lot of cases of gradual change. Farina does agree that we don't have examples for every extant species on Earth right now due to the issues Meyer himself noted -> We are missing samples and transitional forms may not even get preserved.

Farina claims that Meyer refuses to acknowledge the reality of both issues, and instead is lying about the significance of the Doushantou Shale.

Regarding whether Meyer genuinely claimed animals first appear in the Cambrian Explosion...I don't really think that's what Meyer said. Rather, in the video above Meyer says the first (or at least first major) appearance of new forms significantly different from prior forms. So I believe Farina is being uncharitable here.

Similarly, with the number of years Meyer gives for the Cambrian Explosion, to me it seemed Meyer was given an approximation. However Farina does add some details about the potential length of the Cambrian Explosion, and feels Meyer's guesstimate is part of the way ID proponents are dishonest.

Farina further expounds on what he feels is the dishonest tactic. For Farina the central issues about how DI and ID generally portray the Cambrian Explosion are how they make it seem the "Explosion" was akin to a sudden appearance when the Cambrian Explosion is arguably a period of 70 million years.

(At least for me, I don't think I ever felt the ID folk were trying to make it seem the "explosion" was instantaneous, though I have wondered if they were playing "God of the Gaps" here by insisting 70 million - or however long we wish to say the Cambrian Explosion lasted - wasn't enough time.)

The next part pertains to Farina's claim that Meyer's use of the term "phyla" is not in proper accordance to how modern science uses the term. He gives Meyer's definition from Darwin's Doubt:

"The phyla constitute the highest (or widest) categories of biological classification in the animal kingdom, with each exhibiting a unique architecture, organizational blueprint, or structural body plan."

Farina notes that a 1999 paper entitled A critical reappraisal of the fossil record of the bilaterian phyla presents a challenge to Meyer's definition. He specifically notes this quote:

Claims that the phyla are characterized by particular types of ‘ body plan ’ features which putative super-phyletic groupings do not possess (e.g. see Table 2-2 in Arthur, 1997) thus seem to be based on an artifact of how we classify groups of animals : if such ‘ super-phyletic ’ features were readily identifiable, the larger grouping would itself probably be called a phylum, as it would be recog- nized to be phylogenetically unified. As the level at which this ignorance of relationships becomes important is likely to vary between groups, the cladist’s standard criticism that phyla (and other such ranks) should be positively discouraged on the grounds that they engender spurious comparisons between members of the same ‘ rank ’ (see e.g. Smith, 1994, and references therein) seems to be valid.

Farina says the important take-away is that phyla as a designation are "largely arbitrary". As such he believes that rather than worrying about what phyla a particular group of organisms fall into the important question is whether the features they exhibit are explicable under evolution.

He then notes another quote in the same paper:

a body plan is that set of features plesiomorphically shared by extant taxa in a mono- phyletic clade.

Where "plesiomorphically" refers to traits shared by the entire group but are not exclusively unique to that group. He gives the example of insects that share a body plan with all arthropods yet also has identifying features exclusive to its own species.
He then says the terms "Crown Group" and "Stem Group".  Crown Group is the last common ancestor, while Stem Group group refers to extinct ancestors that lack certain features. Farina also notes that the Stem Group could be considered by some to be the very transitional species Meyer thinks are missing from the fossil record.

Farina then shows a clip from another Meyer video:



So now a summary of this video, which will conclude my work on this for now but I'll pick this back up later ->

Meyer says there are two major reasons to doubt Darwinian accounts of evolution. The first is the Cambrian Explosion, which he notes as lasting 10 million years - which would I assume go against Farina saying the period lasts 70 million years. Meyers then notes that not only did this sudden appearance of novel forms trouble Darwin, but it also is a problem for scientists today.
He quotes Eugene Koonin who said the appearance of novel forms was a "Biological Big Bang". I did find a paper where Koonin does use that term:

The Biological Big Bang model for the major transitions in evolution

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal.

The next big reason from Meyer to doubt the Darwinian account of evolution is what he calls the "DNA Enigma". Meyer notes the comparison between DNA and computer code, and how random bits of code should not be expected to produce a better program but an increasingly worse one until the whole program stops functioning. Similarly, he says that it isn't likely for mutation + selection to produce increased complexity that ensures survival.

His reasoning for the comparison is because he notes that for any language, there will be vastly more meaningless gibberish produced than meaningful phrases. (Think Borges Library). He then references Axe's work that argued the probability of being able to produce meaningful/useful DNA sequences would be 10^77 nonfunctional to 1 functional sequence.

Meyer then notes the estimate for number of atoms in the galaxy is 10^65.

So Meyer's conclusion is that there simply isn't enough time for the search space of natural selection to produce the life forms we see today.

Tomorrow we'll continue with the Farina video....like I said this will probably be a very long series of posts but ideally not too many...

So Meyer's conclusion is that there simply isn't enough time for the search space of natural selection to produce the life forms we see today.

To say nothing that even in perfectly controlled laboratory experiments trying to replicate the presumed abiogenesis of life, they always got tar and a combination of differently-handed amino acids. The Neo-Darwinist often falls back on the claim that the produced amino acids are enough evidence for abiogenesis, despite amino acids being only the tiniest fraction of a vastly complex and complicated set of processes needed to even have the basics of a cell.

Besides, biologists studying the hypothesis of abiogenesis can't even agree on the origins of RNA and DNA, nevermind the order in which they supposedly appeared!

To say nothing that even in perfectly controlled laboratory experiments trying to replicate the presumed abiogenesis of life, they always got tar and a combination of differently-handed amino acids. The Neo-Darwinist often falls back on the claim that the produced amino acids are enough evidence for abiogenesis, despite amino acids being only the tiniest fraction of a vastly complex and complicated set of processes needed to even have the basics of a cell.

Besides, biologists studying the hypothesis of abiogenesis can't even agree on the origins of RNA and DNA, nevermind the order in which they supposedly appeared!

I think the origins of life itself will have to wait for the Farina vs James Tour thread, but I'll note that Farina does provide an argument for how nothing about the Cambrian Explosion specifically requires ID. He insists, based on the data, that there's plenty of time and plenty of signs of largely gradual evolution from Pre-Cambrian to Cambrian, and within the Cambrian itself.

I'll get into it later today, it's just a lot of information. I'll also note it's not the final word, Bechly has IIRC 7 articles rebutting Farina's points in this one video. [And Farina has a video that I believe is meant to rebut those articles, will have to see.]

To be honest I expect myself to end up pretty much just as agnostic about biological ID as I am now. However it is pretty educational to finally see what the fuss is about between ID vs RM+NS advocates...though I can't help but wonder how the Third Way folks or other ideas like Platonism of Life Forms or Morphic Fields would affect the conversation. 

My instinct is that both ID and Neo-Darwinism (in the sense that RM + NS suffices) are wrong, or at least incomplete.

Back to Farina's video, at the correct time stamp:

https://youtu.be/Akv0TZI985U?t=1006

A lot of the preliminary stuff is about the first animals...I'm not sure this is all that important because I don't even think Meyer was saying there are no animals before the Cambrian. Rather it seemed to me his point was that the Cambrian marks the first appearance of forms that he believes cannot be derived from RM + NS of prior forms. 

However it does allow us to see the context of Farina's later argument that pre-Cambrian animals evolved into the Cambrian, and the Cambrian itself is a case of gradual evolution taking place as expected though hastened by certain factors.

There are also a lot of papers cited, which I haven't read through. I might do so if it seems warranted after I finish going through this video, Bechly's rebuttals, and then Farina's video rebutting those rebuttals.

So now that I've given some context as to where we're headed, on with Farina's case ->

- The first signs of animals occurs about 650 million years ago due to molecules called Steranes. There are two papers he cites, this one and this one.

-  The presence of Steranes are approximately at the end of the Cryogenian, as the world enters the Ediacaran where we find the first known preserved fossilization of animal forms such as Lantianella, a potential Cn. Farina then provides various examples of such forms. Certain fossils are deemed to be complex enough to be considered animal forms. There does seem to be some potential dispute about certain embryo fossils, but to my understand the general array of animals Farina gives are valid examples of animals in the Ediacaran period, before the Cambrian explosion. Farina cites this paper.

- He also mentions animals who existed in the low oxygen environment of the Ediacaran ocean, citing this paper. Note this part felt important to Farina's argument for why RM + NS can explain the Cambrian Explosion. Eventually there will be more O2 in the ocean as algae develop further.

- 571 years ago we find the first macro-scopic animal communities, as per this paper Farina cites. He particularly notes animal fossils seen in the Avalon, White, and Nama Assemblages. These animals - the Vendian biota -predate the Cambrian Explosion but Farina believes the animals that came during this pre-Cambrian period are of incredible importance to explaining the Cambrian Explosion.

- Farina notes that even Gould thought several of these animal groups were likely protists, lichen, or fungi. However this was in the 80s, and later work would reclassify at least some of these as animals though Farina notes there has been debate about which phyla these creatures should be classified under. Farina then discusses some of the reasoning for classifying certain fossils as animals in academia.

- The reason Farina believes all of this is important is because he feels the evidence is good enough to conclude Ediacaran animals actually evolved gradually across millennia. This progression, according to him, is from soft-bodied rangeomorphs to organic walled non-mineralized forms to hardened biomineralized animals (small shelly fauna). There are also trace fossils of motile animals, with Farina noting that while most Ediacaran creatures perished fossils for a few are found in the Cambrian era. For example Cloudina and Swartpuntia.

Now right before going into the Cambrian, Farina pauses and asks what exactly ID advocates are proposing. Why is the Designer making new creatures during different points of history. For example did the Designer make new creatures at different points during the 3 Assemblages and if so why stagger this out?

While I think that might be a worthy question if someone insists the Designer of biological ID is the Omni-God, I don't know if it's important to the question we're raising here which is whether evolution is best explained by non-material intervention at specific points.

One criticism that might be important is Farina claims here that ID advocates don't even have a clear guide on explaining which creatures were designed and which are just the follow through of an un-guided RM+NS. 

Farina insists ID has no way to explain the pre-Cambrian OR the Cambrian lifeforms.

Next post I'll get into the part of the video that deals with evolution leading up to the Cambrian Explosion.

Time to hit the grindstone again:

https://youtu.be/Akv0TZI985U?t=1681

Farina notes that of the Ediacaran animals the soft-bodied and organic walled fade from the fossil record in the early Cambrian, likely due to the new biomineralized animals. Farina quotes this paper, The Latest Ediacaran Wormworld Fauna: Setting the Ecological Stage for the Cambrian Explosion:

These vermiform organisms were equipped with innovative adaptations of active feeding modes and sediment restructuring capabilities, biomineralized armament against predators, generalist and opportunist adaptability to varying substrates (Cai et al., 2014), sexual and asexual reproduction for enhanced dispersal (Cortijo et al., 2015a), resilience to environmental disturbance (Cai et al., 2010), and presumably high fecundity and rapid achievement of sexual maturity.

This period coincides with the first examples of animals likely preying on others, specifically bore holes in Cloudina fossils.Farina suggests this was due to novel adaptive pressures and this competitive environment helps explain the Explosion.

He also notes animal forms disturbing sediment which disturbed certain bacterial mats varied pre-Cambrian creatures were adapted for.

Oxygen levels also were rising at this time, which would lift size restrictions of organisms. Greater oxygen also allowed for longer food chains and more complex food webs.

Essentially, as Farina explains, given the general rule that 10% of energy stored is available to the next higher trophic level, more oxygen in the water means more levels because oxygen allows for the most efficient way to convert biomass into energy.

Farina notes that apex predators are first seen in the Cambrian, and points out how this could correlate with rising O2 level by looking at polychaetes because increase in O2 leads to their increasing population. This too would result in a spike in competition, which according to Farina sets the stage for the Cambrian Explosion.

Will deal with that tomorrow.

I think the origins of life itself will have to wait for the Farina vs James Tour thread, but I'll note that Farina does provide an argument for how nothing about the Cambrian Explosion specifically requires ID. He insists, based on the data, that there's plenty of time and plenty of signs of largely gradual evolution from Pre-Cambrian to Cambrian, and within the Cambrian itself.

And he then presents nothing to actually back up those claims. With undirected, random, entirely independent and gradual mutations, there is never enough time to create coherent, complex and multilayered structures that have the appearance of being engineered by an intelligence. After all, the humble single cell is vastly more complex than even our very greatest feats of engineering, so intuitively, Farina's claim holds zero weight.

He has to be able to explain how undirected, random, entirely independent and gradual mutations can possibly have such magnificently accidentally potential, especially in a universe that just so happens to have very finely-tuned constants for life.

Even with finely-tuned constants... random, undirected mutations are still the equivalent of billions of monkeys just mashing a keyboard without purpose. The probability of getting something workable in even the supposed lifetime of the universe is basically impossible.

Farina can only claim what he does because he doesn't understand the actual logical implications of his argument. His argument just presumes that life evolved, without first demonstrating that it is even possible or probable to begin with. That's the sad thing about religious ideologies ~ they don't really need proof or evidence, just rationalizations and justifications.

I'll get into it later today, it's just a lot of information. I'll also note it's not the final word, Bechly has IIRC 7 articles rebutting Farina's points in this one video. [And Farina has a video that I believe is meant to rebut those articles, will have to see.]

To be honest I expect myself to end up pretty much just as agnostic about biological ID as I am now. However it is pretty educational to finally see what the fuss is about between ID vs RM+NS advocates...though I can't help but wonder how the Third Way folks or other ideas like Platonism of Life Forms or Morphic Fields would affect the conversation. 

Platonism and Morphic Fields are profoundly more interesting lines of inquiry. They seem to resonate with my spiritual experiences to some degree or another, so I am rather inclined to them in part ~ though I do not think they're the full answer. They just point in directions that seem to make intuitive sense.

My instinct is that both ID and Neo-Darwinism (in the sense that RM + NS suffices) are wrong, or at least incomplete.

ID in the context of a Creator God in a religious sense does feel rather in the wrong direction. Too much grafting of a human personality onto something that, examining the absurdly vast complexity of this universe in scope and size and potential life, must logically not be anything akin to human nor anything close to it ~ but far more transcendent, beyond even the faintest inklings of human comprehension.

Even our own planet is home to lifeforms that defy imagination and comprehension. Even those lifeforms we're aware of and, I think, take entirely for granted.

Even the humble rat is generally extremely intelligent when it comes to problem solving.

And he then presents nothing to actually back up those claims. With undirected, random, entirely independent and gradual mutations, there is never enough time to create coherent, complex and multilayered structures that have the appearance of being engineered by an intelligence. After all, the humble single cell is vastly more complex than even our very greatest feats of engineering, so intuitively, Farina's claim holds zero weight.

Well I am not sure he doesn't present an explanation. At the very least he is providing some reasons to think the Cambrian evolution is gradual and a direct follow through of what happens in the Pre-Cambrian. Of course this may prove to be bad explanations depending on Bechly's rebuttals, but I haven't gotten there yet.

When I get through the whole series and the varied rebuttals from the DI I'll hopefully have a better sense for whether or not complex multilayered structures are able to be achieved by RM + NS or not.

Right now I'm still agnostic about ID at the evolutionary biology level.

Well I am not sure he doesn't present an explanation. At the very least he is providing some reasons to think the Cambrian evolution is gradual and a direct follow through of what happens in the Pre-Cambrian. Of course this may prove to be bad explanations depending on Bechly's rebuttals, but I haven't gotten there yet.

From everything I've read about the nature of the Cambrian Explosion from DI, Evolution News and other sources, there is nothing suggesting it. In the presented time-frames, there is no fossil evidence of any gradualism ~ just an out-of-nowhere fully formed set of modern animal forms that have no explanation. There's nothing even akin to transitional forms, which is why so many Neo-Darwinists just ignore the Cambrian Explosion or gloss it over as "of course it was gradual".

When I get through the whole series and the varied rebuttals from the DI I'll hopefully have a better sense for whether or not complex multilayered structures are able to be achieved by RM + NS or not.

Right now I'm still agnostic about ID at the evolutionary biology level.

Cheers.

Finally we arrive at the Cambrian Explosion:

https://youtu.be/Akv0TZI985U?t=1863

Farina first notes that the Explosion occurred in a series of steps. He first notes the importance of ichnotaxa, which are taxonomy based on fossilized remains. 

Farina notes the first vertical burrowers appear in the Cambrian. The increase in burrowing animals would increase the bioturbation, which in part would create new environments that would result in new adaptations. He then quotes again from this paper:

The initial diversification (Fortunian) is coincident with the appearance of the first sediment bulldozers, but preceded the establishment of infaunal suspension-feeder faunas that were ecosystem engineers of paramount role (Cambrian Stage 2). In turn, the rapid increase in depth and extent of bioturbation associated with these suspension-feeding communities may have triggered another diversification event of biogenic structures that took place during Cambrian Stage 3, and involved the appearance of new behaviours by deposit feeders. Capture of organic particles by suspension feeders allowed enrichment of organics by biodeposition, promoting diversification of infaunal deposit
feeders [50]. Therefore, infaunal suspension feeders may have been ecological drivers of the Cambrian Stage 3 diversification phase of biogenic activity (figure 4), representing a dramatic case of ecological spillover [3].

I'd recommend looking up this part of the paper, as per the video this paper has a nice depiction of the Ediacaran shifting into the Early Cambrian and then the later Cambrian stages.

From this paper Farina claims a large part of the Cambrian Explosion was actually rather gradual, occurring across 541-514 Ma.

He then cites another paper - unsure which one - that divides the Cambrian explosion into two phases, the non-bilaterian dominant followed by the bilaterian. A variety of stem group animals go extinct in the first stage due to the Sinsk Extinction vent, which then allows the crown group to dominate. I don't believe it's the same paper but here's a paper about this division of the Cambrian Explosion into two phases.

Next post will get to the part Farina takes on Meyer's view of the Great Ordovician Biodiversification Event (GOBE).

(And if anyone is worried I'm not presenting the ID side in all of this, I do plan to do that after I go through all the stuff in this video. Bechly at DI wrote 7 articles about this video, to give you a sense of the amount of content that has to be taken into consideration.)