Farina vs Stephen Meyer

Farina's criticism of how Meyer interprets GOBE as the appearance of new forms that cannot be accounted for by evolution (recall the Bechly rebuttal to Farina will be posted after I finish summarizing the video):

https://youtu.be/Akv0TZI985U?t=2314

Farina starts with defining the Great Ordovician Biodiversification Event, or GOBE, as an evolutionary event happening after the Cambrian where the more generalized fauna of that era end up developing into more specialized marine fauna that would remain common through the Paleozoic era.

The GOBE occurred in two phases, the early Ordovician with some diversification and the middle Ordovician that saw a sharper rise in diversification. Farina then mentions certain species that arrived during this period such as stromatoporoid sponges, encinoderms, ostracods, corals, trilobites, bryozoans, nautiloids, and brachiopods.

Farina notes that the actual events of the GOBE doesn't fit what he believes to be Meyer's "phyla level intelligent design". The radiation (in a biological sense) of this time period is gradual and extends from the Cambrian. He then defines two terms:

Disparity - Differences between Clades

Diversity - Differences within Clades

So the Cambrian is an Explosion of Disparity, while the GOBE is an Explosion of Diversity. Farina then says in Meyer's terms this would be new body plans in the Cambrian, versus variation in the body plans in the GOBE. Farina then claims no known new phyla appeared in the GOBE. He then shows the evolution of trilobites, which says can be seen from the fossil record to occur without any Intelligent Design at all.

He then notes the biological/evolutionary radiation of the Crown Group in the Cambrian lasts until that era's conclusion, and then continues on in the post-Cambrian where the GOBE occurred. He notes this shift is so "seamless" some even include the late Cambrian as part of the GOBE.

Farina then cites a paper - this one I think, which is sadly pay walled - that notes the GOBE lasted approximately 30 million years, followed by an extinction event at the end of the Ordovician, followed by new diversification of biological forms during the Silurian. He mentions this because he feels the record shows continuous natural processes rather than the sudden conscious intervention for the production of new animal forms.

Farina then wonders what Meyer means when he says the first insects appeared without predecessors, because arthropods evolved in the Cambrian and the insects within that phylum. The last common ancestor of hexopada - insects their closest relative species spring tails - lived in the early Ordovician, while the last common ancestor of all insects lived in either the later Silurian or early Devonian. The earliest insect fossil is a pair of mandibles from Scotland, dated back to 412 million years ago (the Paleozoic Era). The earliest winged insect fossil dates to the Carboniferous which is about 324 million years ago.

(Note that he mentions these timelines are constructed with the help of "molecular clocks")

Farina also notes that as insects are within the Crustacea sub-phylum, in only makes sense that we see fossils of early crustaceans such as ostracods before we see insects. Farina then notes the major differing characteristic between insects and their fellow arthropods is their wings. So insects are a diversification of arthropod body plans, using Meyer's terminology, which would further suggest there's no need for any Design intervention. (At least according to Farina)

Farina realizes ID advocates will then ask about the evolution of the wings, but he notes this is actually understood very well rather than being a mystery which requires Design. Citing this paper, Farina notes that research into the genetic development of wing formation suggests certain vestigial genes were exapted for a new process - that of flight - across years on the evolutionary scale. Additionally wing formation involved merger of tissues from the limbs and abdomen.

He notes a similar story with dinosaurs, which as amniotes evolved from reptiliomorphs. Amniota, over evolutionary history split into two major groups - Synapsida (from which mammals evolved) and Sauropsida (from which we got dinosaurs). Additionally Sauropsida would end up giving us bird and reptile species. Farina notes these transitions are documented in the fossil record as being slow & gradual.

Farina then notes that the fossil record for turtles shows varied intermediary forms evolving gradually across time, with the same being true for birds which go back to the fossils of feathered dinosaurs. He also mentions that scales and feathers are made of the same protein, and that single point mutation can cause chickens to grow feathers where you'd expect scales.

Farina notes the fossil record also contains the gradual evolutionary story of marine reptiles. He does accept there has been some mystery about exactly when the first flowering plants appeared, but that recent research is zeroing in on the timeline. He also notes that flowers appeared due to known evolutionary transformations of existing leaf structure, thus not - in his opinion - requiring a Designer at all.

He notes there's even more about plant evolution and biology in his botany series.

Thus, according to Farina, there are documented transitional species in the fossil record for flowering plants, insects, birds, reptiles, amphibians, and more. As such, if he's correct, it would seem there's no Design needed to explain any of the examples Meyer gave as supposed novel forms.

As a special point he notes Meyer is wrong about when the first mammals appeared, by about 100 million years.

Next post will get to what Farina believes Meyer gets wrong about genetics. Thankfully I believe this is the last topic of the video, and once I finish summarizing it I'll get into Bechly's rebuttals...and then Farina's rebuttal of Bechly...

Final part of the video, set to the correct time stamp:

https://youtu.be/Akv0TZI985U?t=2907

Noting once more that biology is not my best subject, so any corrections/clarifications much appreciated!

So before getting to Farina's criticism, just to recall Meyer's point about information in biology is connected to information in software. Starting with the video Farina is talking about that I mentioned above in the opening post, but reposting now with the correct timestamp ->

https://youtu.be/aXKAMR94-rc?t=843

Quick summary -> Meyer says that just as you have to add information to a computer program to expand it so too must a Designer add information to the existing biological forms. Meyer then claims explosions of form are in tandem with injections of biological information. Meyer also believes biological information can be seen as parallel to digital & linguistic information (books, hieroglyphs, etc), the latter which we know has to originate from minds. Meyer specifically uses the example of a stomach and digestive enyzmes as a case of a higher level, more complex biological form.

Now back to Farina's criticism ->

Farina objects to the supposed analogous relationship between computer code and DNA code. 

Farina starts by noting that enzymes could come first, and then end up being utilized adaptations until we get to the stomach. He notes stomachs began as gastrovacular cavities and then evolved into stomachs of different animals.

Farina claims that Meyer's idea of information means that information is a material substance that must be created. (Note: I don't think this is what Meyer is actually saying.)

Farina says it's better to think of information simply as a pattern or sequence of items. He gives the example of a sequence of DNA nucleotides and says this would count as information simply by being the template for protein synthesis, and this is all done without any need for a Designer.

Farina then objects to Meyer's analogy of adding random changes to a computer program being more likely to ruin a program than to create a new program. For Farina the issue is that to him neither biology nor computer software actually work this way. Farina notes that self-modifying programs with the correct feedback mechanism in place actually do get better across time, just like evolution.

Farina then gets back to DNA, claiming that Meyer wants us to believe lots of random mutations are happening in any one organism - that would be the equivalent of the kind of mutation and ultimately likely death of someone suffering from radiation poisoning. Instead Farina says we should think of mutations cropping up very slowly, with some being advantageous, some disadvantageous, and some neutral.

Farina notes that mutation + natural selection works so well that the same principle is used to engineer enzymes in the lab.

Farina then challenges Meyer's claim that mutations degrade information while minds generate information. To Farina, "mutations degrade information" is a meaningless statement that can only be useful in deceiving those ignorant of biology.  Instead we should look at the way mutations actually occur as changes in the nucleotide sequence of DNA. Farina then notes he has a video that goes into more detail, while providing a short summary.

So here's the video:




The summary just covers the basic steps but I'd recommend just watching the above video since it's under 7 minutes.

Farina then notes the benefits of mutation through natural selection are seen in bacteria & viruses every single day.

Farina contends Meyer wants to view information as something separate from the DNA, rather than accepting information refers to changes in the DNA. (I believe this gets into the question of Information Realism?)

The main point here being that mutations simply change the information, they don't "degrade" it.

Farina then challenges Meyer's claim that unless the chemical letters in DNA are sequenced properly a protein molecule won't form. According to Farina so long as the DNA sequence has a proper start codon you will have a protein molecule form.

Regarding Meyer's claim that sequences that produce stable proteins are incredibly rare, Farina in fact denies the very idea of "unstable" proteins based on the above.  Farina claims every codon - three letter sequence - will produce a protein. Since these proteins don't just bizarrely fall apart Farina says the very idea of unstable proteins doesn't make sense.

Farina then assumes Meyer really wanted to say that very few proteins have biological function. He then challenges Axe's claim - which Meyer references - that for every functional protein sequence there are 10^77 non-functional protein sequences.

Farina claims that since Axe didn't actually make all those sequences he cannot really say whether they are non-functional. Farina believes what they want to say is that a change in the sequence would negate the proteins original function, however even there he believes Axe and Meyer are wrong as a singular shift in a particular amino acid chain would not by necessity destroy its original functionality.

He then notes that the 20 amino acid chains are actually quite similar, and as such you could actually swap many of them without loss of original function. The exception being key residues and active sites.

Farina then gives the example that enzymes can have different sequences in different organisms yet fulfill the same exact function. He also notes that neutral mutations are why we can utilize molecular clocks.

Farina then goes on to attack Meyer - and I guess DI's - ideas about mutation. He notes there are not just point mutations - which he feels is the focus of DI - but various kinds of mutation:

- point mutation, change in a single base pair
- deletions/insertions of a base pair
- inversions, where a segment of a chromosome is reversed
- transpositions, where genes shift to another position in the genome
- duplications, where one or copies of a segment are produced

Farina says that biologists on the whole accept mutations occur randomly due to exogenous mutgens or replicative error. He also notes that recombination of genetic information can also lead to mutations - as such many organisms will experience mutations during embronic development.

Through this RM+NS process, mutations are harmful lead to less probability of survival and beneficial ones lead to increased probability of survival and thus passing on of genes. There are also neutral mutations, which may be carried across generations until they lead to beneficial or harmful outcomes depending on environmental pressure.

He notes of the most famous observations of beneficial mutation comes from observation of E.coli bacteria, where he cites this paper. A bacteria population developed the ability to metabolize citrate in an aerobic environment. Even without a new gene, a duplication and transposition mutation conferred new benefits.

He further notes that looking at embryonic development as it exists today shows how major changes can occur in body development, which he believes counters the DI claim that novel organ systems appear in the fossil record without good explanation from evolution based on RM+NS. He notes that it is actually a surprisingly small number of genes that coordinate body plans, I believe citing this paper.

He also challenges Meyer on the Waiting Time Problem, referring to a video made by another ID skeptic "Theevilutionist":




To summarize briefly because I already know Bechly is going to get into this in his rebuttals to Farina: Creationists (which I guess includes ID advocates?) believe the time to get and coordinate beneficial mutations to produce life as it currently exists would take too long just going on RM + NS.

Theevilutionist says what it comes down to is just about every Creationist (again, this includes ID advocates) - or at least those who want to participate in legitimate science discussions - believes in some degree of evolution. So to him it's a "What's the Barrier" question, because if you accept evolution in some cases why is there a problem for other cases at larger scales across greater time periods. The argument of ID advocates (and I guess some Creationists) is that mutations are largely harmful - "Darwin Devolves" - which means you can't have long term macro-evolution where we see novel forms due to speciation. There's also Irreducible Complexity, which he says isn't a problem and he's addressed it another video....which maybe we'll get to down the line...

So the Waiting Time Problem is another barrier proposed by ID/Creationism advocates. This takes a few different forms:

- A feature with specific characteristics would take too long to evolve
- A speciation event would take too long due to too many differences
 
Theevilutionist then offers his rebuttal. First he notes these arguments ignore that mutations can occur in parallel rather than sequentially, then he notes they also ignore recombination with some excuse making for why they do so. Yet recombination, in his opinion, cannot be ignored and when factored in reduces supposed Waiting Times. He notes that recombination via sexual reproduction has a lot of risks and energy costs, yet so many animals evolved to reproduce this way because of the benefits of recombination.

The third error, in his view, is that ID/Creationism advocates assume a specific target sequence and then look back to try and find the odds of having it occur within the standard accepted time frame of RM+NS evolutionary biology. Instead the reality is many different sequences can actually serve in the same functional capacity. He notes this has actually been shown by experiments on E.coli, where you can replace functional sequences with random ones and found many could serve the same function.

Then looking at the human & chimp genomes, where the ID/Creationism advocates claim the differences are too vast to be achieved under RM+NS alone. This he feels ignores the fact that the measurement of difference should not be between modern chimps and modern humans, but instead a measure of difference of both from their common ancestor.

He also feels they assume all changes have to be beneficial, and thus confer survival advantage. However modern studies show that many mutations aren't necessarily harmful or beneficial, so can't be used in a proper calculation of Waiting Time. Given that scientists due have some means of tracking positive mutations, he believes the differences that need to be explained by natural selection is actually much, much lower than what ID/Creationism advocates want us to believe. (About 10 times lower even if you multiplied the number of accepted beneficial genetic differences by 10.)

That concludes the summary of this video cited by Farina, will get into the final minutes of the Farina video in the next post.

That concludes the summary of this video cited by Farina, will get into the final minutes of the Farina video in the next post.

I believe most of Farina's rebuttal of the Waiting Time Problem is covered in the prior post summarizing the video from Theevilutionist.

However, I think one point not covered there was polypoidy, which has led to observable speciation in plants but also the marbled crayfish.

Farina also mentions mutations in Thamnophis, the genus of garter snakes, developed a resistance to newt toxin due to a combination of point mutations.

Many gene sequences are shared across the evolutionary tree, including a sequence for pyrimidine biosynthesis that humans share with amoeba.

Finally Farina alleges that "genetic information" is a vacuous term, because it's not clear how to assign a metric of information to DNA sequences. Does it depend on length? On the processes a sequence is utilized for?

Farina claims there is no good way to assign such a metric, and rather what we can do is try to determine how many mutations occur between - for example - a fin & an arm. Which is why biologists - according to Farina - talk about genes and mutations, rather than genetic information.

That is the conclusion to the main arguments, there's some stuff at the end about how dishonest ID is but it's more accusation at this point given Farina believes he's thoroughly debunked Meyer's claims.

Of course we will have to get into Bechly rebuttals to see how true this is.  

As an addendum I will note the question of whether mutations are totally random has been question[ed] by non-ID biologists Levin and Wagner who - as previously mentioned - think some Platonism of Forms may narrow the search space. Kastrup believes we can't be sure if mutation is random:

However, an extra idea is often conflated with the foregoing: whereas natural selection is demonstrably not a random process, the mutations underlying the process are consistently assumed to be. The problem is that evidence for natural selection is not evidence for random mutations: nature will select for survival fitness whether the mutations themselves follow a trend or not.

To demonstrate that the genetic mutations underlying evolution are random, one would need a fairly complete record of (a) the mutations themselves, as they occurred throughout the history of life on Earth, including those discarded by natural selection; and (b) the corresponding phenotypic characteristics. Only then could one run a randomness test to verify that no phenotypic trends are present before natural selection plays its role. Of course, the fossil record is far too sparse to allow for such a test.

So the assumption that genetic mutations are random has, strictly speaking, no empirical basis. Its motivation is merely subjective: many cannot fathom any plausible mechanism that could impart a pattern on the mutations themselves. Compelling as this may sound, lack of imagination and a subjective sense of plausibility aren’t valid reasons to pronounce scientific facts.

Probably going to be a few days or longer before I get into Bechly's articles.

Anyone else should feel free to address any of the points Farina has made [but please focus on the points in the video, not the general stuff that we have another thread for]. I'll say for me personally the ID case was never something I thought was exceptionally strong so I was open to seeing it challenged.

Still having gone through this video over the course of several days I don't think Farina presented a knock out case.

I will say I didn't realize so many sequences could fill the same role in an organism. It does seem like the Waiting Time argument from ID advocates is not as strong as they might want, but I know Bechly addresses this so I don't want to make a conclusive judgement.

And as @Valmar noted ID can have many different meanings. For example if we did accept Levin's argument that Platonism of Forms narrows the search space, this then leads us to ask about the nature of these Forms. Is a Form a mental entity, and thus residing in a Mind? Or can there be Platonic Forms existing "out there" in some reality...I actually cannot recall what Plato himself thought as he does get into some theisitic concerns in the later Dialogues IIRC...will have to check...