A Long Story of Misunderstandings and Futility & An Invitation to "Long Story Short"


It has been a while since I have posted something on the League of Reason. A lot has changed indeed.

For more than a year now, along with others I have helped with Jackson Wheat as an editor for the scripts of his videos. Last year in August, we came across a channel that had (at the time) only one uploaded video. It's called "Darwin’s Biggest Problem | Long Story Short: Evolution" made by someone called "Long Story Short" (LSS). When I first watched the video, I was impressed by the art style and his witty manner of speaking, although that's pretty much all I can say about it that was positive. The content was your typical creationist dribble on the "Cambrian-SPLOSION" [Though LSS has objected to being called a creationist]. In fact, we recognised that some of his arguments were taken from Stephen C. Meyer's "Darwin's Doubt". So, Jackson Wheat published a two-part rebuttal video.

Which led to an online discussion between Jackson and LSS in September. It was okay, he mainly stuck to the point, though it mostly didn't go anywhere eventually. At the end, I asked Jackson to notify LSS about his outdated citation from 1993, which he uses to claim that the Cambrian Explosion lasted for "just" 6-10 million years - which is obviously intended to mean "too short" for evolution.

However, quoting from the paper.
Analyses of the Cambrian faunal radiation indicate that diversification followed a logistic pattern of increase (1,2,34,35). Our calibrations shows that the initial (Manykaian) interval of slow diversification followed the ediacaran faunal epoch by no more than 20 million years (m.y.) and lasted approximately 14 m.y. In contrast, if we accept the age of 525 Ma for the Atdabanian-Botomian boundary, then the Tommotian-Atdabanian period of exponential increase of diversification lasted only 5 to 6 m.y. In any event it is unlikely to have exceeded 10 m.y.
Note that there was an initial “slow” diversification of 14 million years before the exponential increase of 5-6 million years. That’s already 20 million years in total. And what’s more, note that they accepted an age of 525 Ma for the boundary. That paper was from 1993. The Atdabanian-Botomian is now dated to 516 Ma. So the period of exponential increase lasted from 530 to 516, which is 14 million years. That's 28 million years in total. Is that still "too short"? I have no idea what he would consider it to be too short.

Then a few months later in January, LSS made another video, this time on homology, titled "Is Homology Evidence for Evolution? | Long Story Short". He makes the argument that using homology as evidence for evolution is circular reasoning - and more. Not only that, it was published on the Discovery Institute's Youtube Channel. Yeah, that's right, the one that doesn't do much discovering. This video also needed to be correct, so Jackson Wheat published the following:

This time, it didn't led to a discussion on a live hangout. Rather, LSS replied with a response video:
"Answering bad arguments for evolution: homology. | Long Story Short"
Oh boy was it bad. LSS omitted the very substance of Jackson's arguments. Very often, he simply does the following:
Step 1: Play a short clip with Jackson expressing his disagreement.
Step 2: Cut off right before the explanation FOR the disagreement.
Step 3: Proceed with an objection to the disagreement (often by reasserting the same argument),
which was (frequently) already addressed by the explanation that was cut out in step 2.

He also made one of the silliest claims I can think of, like how the platypus is supposedly a "chimera" that doesn't fit in the evolutionary phylogeny. I wrote a detailed rebuttal, which I linked it in the description of LSS's video. I got the following responses:
LSS: Thanks Nesslig, some genuinely fair points but I'm afraid we're largely talking past each other. If you and Jackson can ease up on the name calling and accusations maybe we can have a reasonable dialogue, but we're not going to get anywhere with this sort of thing.
ME: What "names" did I call you? At what point did either me or Jackson call you "names"?

LSS: Do you really not know? You, Jackson and other commentators frequently pull the creationist card and all the caricatures and tropes associated with that (as if I've ever said anything about that or ever appealed to any religious document or belief). And you're also very quick on the "misleading" "misrepresenting" and "quote mining" labels — these claims are all spurious as far as I'm concerned and mere emotional insults. They generate more heat than light, as they say.

You also claim that I'm not listening and cutting Jackson off (when I specifically link to his video and encourage everyone to watch it). In this doc you interestingly try to psychoanalyze me as well as ruminate about my motivations and attribute other fallacies to me. Just a quick scan and I'm noticing many things we would agree on (but you seem to think we disagree), but also substantial problems with it (where you completely misunderstand my point), I'm happy to have a polite conversation but not if this is what you have in mind. I want to discuss the facts of the matter rather than the sociology involved.

ME: I cannot say for other commentators [obviously]. But neither Jackson nor I have called YOU a creationist. When Jackson stated at 9:28 "This is really rich coming from creationists, yes creationists, look up the Discovery Institute's wedge document " it was in reference to...well...the Discovery Institute (as your video was firstly published by them). If you say you are not a creationist yourself, I will take your word for this, but I cannot do the same thing for the Discovery Institute. See point #14
You did make misleading arguments, you also made several misrepresentation and you made quite a few quote mines and fallacies. None of these are "name calling" nor do they necessarily imply malicious intent on your part. They are criticisms, don't take it personally.
You cut Jackson off right before he could explain the points he made. Like when you said at 2:25 that you weren't sure how you incorrectly framed Berra's analogy...right after you cut him off before he explained how you did framed it incorrectly. And this isn't the only instance of something like this happened. Just because you linked the video in the description, that doesn't automatically absolve your video from any wrong doings such as these.
I never questioned your own motives. I did say that I suspect you are "possessed by Morton's demon", which is a reference to "conformation bias", however confirmation bias is not a "motive". Besides, I also said my opinion on that [is] not important, as it is just my opinion. What is important is the fact that your video contains numerous errors and misrepresentations. And that's what I focused on for the entire response.
I am also happy to discuss the facts, but not when you take everything as a personal attack like this.

Right at the beginning of March, Jackson also published a rebuttal to this, which also is a good summary of the rebuttal I wrote.

Now, little over a week later [today], LSS made another response video.......
.......this is where LSS went into a nose dive for the worst.

[continued in next post, due to size limit]
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This video:

Is probably one of - if not THE - worst response videos, or videos on this topic in general, I have ever seen. I was already expecting something bad in response to the latest video that Jackson uploaded, but not of this calibre. Though that is my opinion and I will let you be the judge of that. Here I will go over the points he is making here.

1st: Still being distracted by the Haeckel side-note [0:22 - 0:53]
In Jackson's FIRST rebuttal, his first point was that the significance of homology as evidence of common descent isn't just the"similarity". It is the PATTERN of BOTH similarities AND differences. With that he uses couple of examples of similarities and differences and during that, he made a quick side-note that Haeckel noted that whales were closely related to hoofed mammals. For context, I will quote Jackson from the FIRST rebuttal video: I colour coded the text for LSS so he can see the difference between the: Actual point especially this part - Examples - Side note
I would add that the significance of homology with respect to evolution and common ancestry isn’t merely noticing some similarities between different organisms. The differences also matter. In the common example that LSS uses, we can see many differences between tetrapods limbs. For example, in birds the digits, carpals and metacarpals are fused forming the carpometacarpus. This is a trait that is only shared by birds. When we compare the limb structure of tetrapods with the appendages of other vertebrates, we see what makes the structure of tetrapod limbs unique. The flippers of whales and sharks look similar on the outside and they perform similar tasks, but the internal structures are very different, that of whales being more similar to us than to sharks. This is just one reason why we know that whales are tetrapods. In fact, as far back as the late 1800’s, naturalists like Ernst Haeckel recognized that whales are closely related to hooved mammals. So we have many similarities and differences among different organisms, but what makes them relevant is their pattern among living things. Humans have noticed this for ages, but Carolus Linneaus was the first to construct a method of classification to describe this observation. He didn’t find that animals were classified as distinct “kinds”, instead they formed a nested hierarchy. No one knew why life was organised this way. This is where Darwin came in. The distribution of organismal traits forming a nested hierarchy, wherein each group has its own unique set of traits that are shared by its members, is exactly what is expected from evolution and common ancestry. This is why Darwin used these traits that were labeled homologous as evidence for common descent. Basically, with his method of taxonomy, Linneaus constructed an evolutionary tree without even knowing what it was.

The part of Haeckel was NOT the point of Jackson's argument, nor did he use that to support his point. This has been explained to him in the second rebuttal and in my response document - but LSS still thinks that he "summarised" Jackson's argument when he focuses on it, so he is missing the point completely.

Also, nowhere did Jackson rule out other explanations for these similarities "A priori" as LSS claimed he did. Again, the point was that the pattern of BOTH the similarities and differences form a nested hierarchy. Common descent PREDICTS such a pattern, but "intelligent design" does not predict this. That's why homology (as in the traits shared by members within Linnaean taxonomic groups which form a nested hierarchy) is best explained by common descent and not by intelligent design.

2nd: But....but....HE USED PICTURES OF CLADOGRAMS!! [0:53 - 1:31]
Jackson explained that we wasn't using cladistics to support the reality of a nested hierarchy - as he mainly focuses on how Linnaeus had already recognised this pattern centuries before cladistics was a thing. Here, LSS objects. He insists Jackson was arguing from cladistics because Jackson......showed a picture that contained cladograms.

Yeah, I know....it is a stupid objection, one that I preemptively addressed in my response document (see point #2). LSS disregards what Jackson was actually talking about, you know, how Linnaeus didn't saw the distinct "created kinds", and found a nested hierarchy instead, and all that. Also, Jackson FIRST used a picture of a nested hierarchy - one that wasn't a cladogram - ....in fact...if you listen carefully during the transitions from one figure (the non-cladogram) to other (cladograms), you hear a clear shift in what Jackson is talking about: He goes from first explaining Linnaeus' observation of a nested hierarchy; to explaining why it supports common descent.
So we have many similarities and differences among different organisms, but what makes them relevant is their pattern among living things. Humans have noticed this for ages, but Carolus Linneaus was the first to construct a method of classification to describe this observation. He didn’t find that animals were classified as distinct “kinds”, instead they formed a nested hierarchy. No one knew why life was organised this way. This is where Darwin came in. The distribution of organismal traits forming a nested hierarchy, wherein each group has its own unique set of traits that are shared by its members, is exactly what is expected from evolution and common ancestry.

This is why Darwin used these traits that were labeled homologous as evidence for common descent. Basically, with his method of taxonomy, Linneaus constructed an evolutionary tree without even knowing what it was. Please note the emphasis on the nested hierarchical pattern of these traits, which will become important later on.
And a cladogram IS in fact a good illustration for why common descent EXPECTS a nested hierarchy. LSS has no grounds to complain about using a picture of a cladogram for this purpose.

LSS says he doesn't know what Jackson wants to accomplish by distancing himself from cladistics. Jackson doesn't want to distance himself from cladistics. It's just the fact that THIS wasn't the point of his argument. The observations that Linnaeus made was the point. So Jackson was AVOIDING something irrelevant to the actual point. This is also the reason Jackson didn't address LSS's complaints of cladistics. As he has said at the start of the video, Jackson was trying to be as brief as possible, so he left out things like these that were beside the point. Furthermore, he also referred to my response document for a FULL response, where I DID address his complaints.
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3rd: The nested hierarchy...illusion useful for categorising...or an actual thing? [1:31-1:47]
Here LSS grants that Linnaeus recognised a nested hierarchy of life...a pattern that is exclusively predicted by common descent...but LSS objects to that by asking whether these patterns are "merely useful for categorising or do they show actual history". Basically he is asking whether this pattern isn't just a mere illusion - an artefact of classification - like how humans tend to classify all sorts of things that have no common ancestry. Creationists often use examples such as cars and planes to assert that taxonomy doesn't support common descent since anything can be forced into a nested hierarchy. I addressed this in my response document (see point #2) specifically the 3rd point on his objections on cladistics. The pattern that we observe in designed objects are not at all what we observe in living things. Designers are free from the limits of phylogeny. Life forms evolve change via a succession of slight modifications that are inherited from their ancestors, such that complex structures are build upon of modified from what is already inherited. Designers on the other hand can start entirely from scratch or reuse or swap parts from different such that it produces chimeras, designs with a mix of different things that don't fit in a cladogram. This is why any fictional creature humans have imagined will almost always violate phylogeny - like the pegasus.

A good video in this point is AronRa's falsifying phylogeny

This is why cars and planes DO NOT actually fit into a nested hierarchy. And the fact that we don't observe these absurd mosaicism shows that the nested hierarchy that Linnaean recognised [without having an evolutionary-bias] is real, and not just made up for the purpose of classification. And no, the platypus is not a chimera (more on that later). Besides, nested hierarchies aren't the only form of how you can classify organisms. Creationists are now all on about their "baraminology", which is only a nested hierarchy "within kinds" but not "between kinds". But then at what point does this nested hierarchy stop? If some life forms ARE related to each other, but some aren't, then it should be easy to pin point where these relationships end, yet they don't have an answer. That's AronRa’s Phylogeny challenge or Jacksons’ Baraminology challenge. And this also applies to someone who is not a creationists but still denies common descent like LSS.


4th: Misunderstanding Doolittle...so typical [1:47-2:10]
Then LSS proceeds to talk about...again...the incongruence between conflicting trees from different genes showing that phylogenetic is all
"just molecular cherry picking. A a big wet blanket for the hopeful biologists. These incongruences has crushed their hopes like a soggy old grape"...It's the same claim over and over again. He just finds new articles that he doesn't understand and thinks it supports his case. Here he cites an article (one that he hasn't cited before), from Ford Doolittle. Anyone familiar with him and how his work is abused by ID/creationsts this knows where this is going.

As LSS quotes from the abstract:
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.

in my response document (see point 13#) I have said this to LSS:
I have noted a trend wherein all your own citations all make, at the very least, much more nuanced arguments or, at worst, they outright contradict yours. The problem that you are dealing with is that you don’t read the papers themselves. You just select a few quotes, which in isolation from the rest of the paper somewhat concord with your own beliefs, and then you jump to the wrong conclusions based on your own preconceptions. And quite often these preconceptions are refuted by the very papers that you quoted from.

This is another example. Notice what follows RIGHT AFTER the quote he mined out of the abstract.
This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.
Doolittle's work is constantly quote mined in order to support the claims against common descent, and that is what LSS just did. He quoted that and used it as evidence against common descent (or rather against the nested hierarchy and by extension against common descent). However, here it is already clear that Doolittle doesn't agree with this. In fact he says that this DOES NOT lead to the conclusion that LSS desires. What Doolittle points out is the significance of other mechanisms, those that causes genetic sequences to not always fall within - or be inherited such that it forms - a perfectly bifurcating tree-like pattern.

Basically, in relation to LSS's claim:
If Darwinism [he means common descent] is true, we should be able to construct reasonably consistent family trees pretty much no matter what genes we compare.
Doolittle is saying: NO, that's not true. There are other mechanisms that are relevant which means that we actually DO NOT EXPECT what LSS is expecting from what he calls "Darwinism". His own citations refutes his misconceptions...again....And it is the same thing that we have pointed out in Jackson's FIRST rebuttal.
“If Darwinism is true, we should be able to construct reasonably consistent family trees pretty much no matter what genes we compare. But that’s far from the case”

The words “reasonably consistent” and “pretty much no matter” are doing some heavy lifting here. Evolution certainly doesn’t predict that every single phylogenetic tree inferred from every single individual gene will give the exact same result, so contrasting one “correct” result (cytochrome C) against one “incorrect” result (cytochrome B) doesn’t exactly do the subject justice. It reminds me of when news shows present a “balanced discussion” between one expert and one crackpot – a 50:50 split is not representative of reality. Evolution predicts that neutrally evolving DNA sequences will record common ancestry, not necessarily individual genes. Genes are functional sequences by definition, and over the course of evolution selection can act on them, which disrupts the “true” phylogenetic signal. There are also other biological phenomena that are known to disrupt phylogenetic trees, like horizontal gene transfer and incomplete lineage sorting.

SO, LSS is using his own misconceptions as the basis for his claims that the genetic "incongruences" are evidence against "Darwinism". But it is not evidence of that sort. It only demonstrates his own ignorance on what he is trying to argue against.

Furthermore, notice when Doolittle said "such data sets" and "at the base of TOL" and "what we know about [the] process" So What is Doolittle specifically talking about here?

In short, Doolittle argues that the tree of life isn't a "tree" at the single-cellular prokaryotic level. Horizontal gene transfer causes genes to be...well...transferred from one lineage to another, sometimes to distantly related organisms. To give an illustration, Doolittle points out that due to process such as horizontal gene transfer, the tree of life - at this scale - looks more like this.

The figure is taken from Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000) For more details about this, See Laurence Moran blog post. This isn't exactly a picture that LSS likely would have in mind with a common designer designing life forms independently. While Doolittle has argued that this shows it isn't a "tree of life", others like Daniel dennett have said that it is still a tree, but more like a banyan rather than an oak. Others have called it a web, or a coral, but in all cases...Common descent is still there, but the pattern may be different that what was initially thought before we knew about HGT. LSS may be jumping up and down in joy and say "HA HA!! No nested hierarchy you see?!" but he should note that this only applies at this scale. As Doolittle ALSO explained in the article that LSS cited:
“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.”
When you think about only eukaryotes, horizontal gene transfer is very reduced, due to the nucleus. And it is even more reduced in multi-cellular lineages (see the text in the figure). As Doolittle explained in another article from 2009:
“In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not.”
HGT occasionally happens in animals, mostly in the form of retroviruses, which is obvious since they have to insert their genome into that of organisms in order to replicate themselves. However, genomic remnants of retroviral insertions in our genome, is far from being evidence against common descent, or the nested hierarchy for that matter. They actually support common descent.
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5th: When you don't have good a counter argument, just say "nuh-uh" [2:10-2:35]
LSS framed Berra's analogy - AS IF - it was intended to be an answer the question
What is the proper explanation for homology - common descent or common design?

Here is the full context of Berra's analogy
“The accelerating pace of hominid fossil discoveries is truly dazzling. In Darwin's time, only a few Neanderthal remains were known, and they were misunderstood. Today we have a whole cast of characters in the drama of human evolution. These fossils are the hard evidence of human evolution. They are not figments of scientific imagination. If the australopithecines. Homo habilis and H. erectus, were still alive today, and if we could parade them before the world, there could be no doubt of our relatedness to them. It would be like attending an auto show. If you look at a 1953 Corvette and compare it to the latest model, only the most general resemblances are evident, but if you compare a 1953 and a 1954 Corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious (Figure 41). This is what paleoanthropologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people. There are quibbles about individual relationships, but each new discovery helps fine-tuneour increasingly detailed knowledge of human evolution.”

As we have explained several times to him, Berra did NOT use that analogy for this purpose.
the way LSS frames Dr. Berra’s analogy is quite misleading, making it seems as though the Corvette analogy was specifically intended as an argument for why homology is best explained by common descent and not by common design. Instead, Berra used it in his 1990 book to get across the idea of how successive slightly different forms (as seen in the fossil record of human evolution) eventually lead to quite different appearances. [...] That was the point of the analogy. To convey the concept of gradual succession towards increasingly different forms, he made it more easily understandable for the layman by giving a more familiar example. It wasn’t presented to explain the evidence and certainly not presented as evidence for common descent over design, not even remotely.
And me in my response document #3
To reiterate, the point of the analogy was to convey the concept of gradual change of forms that form a gradient. Looking at these fossils from older to newer is like looking at these different models of a car from older to newer. Although, I personally find this analogy itself over simplistic since the hominin fossil record isn’t a single line of “progression” (it’s a branching tree after all). However, It was NOT intended to answer the question “does evolution or design best explain homology?” like you framed it to be.

That's not to say I don't have issues with Berra's analogy. As I have said in my document:
1: I personally find this analogy itself over simplistic since the hominin fossil record isn’t a single line of “progression” (it’s a branching tree after all). And 2. Berra used “descent with modification” very figuratively when he described the cars (I am pretty sure he doesn’t actually believe that cars procreate).

But these aren't the points that LSS made. He mis-framed Berra's analogy as if it was intended to be an answer to the question he asked. That's the mistake he made, but after multiple attempts of us trying to point this out to him, it is clear that LSS shows no interest in actually listening to what we have to say, let alone make an actual respond to our points. He basically responds with: "You can keep arguing Berra didn't mess up, but he did mess up, I am right, you're wrong...lalala" I am sorry LSS, but is just an assertion, NOT a response to our rebuttal!!

6th: It's a question...and it is not faulty. [2:35-3:05]
Jackson asked a question:
Why wouldn't the designer design life forms in literally any other pattern from what is expected of common descent.
LSS responds (in the first time) by saying:
Jackson makes a faulty assumption that a designer would design de novo or from scratch rather than from a common pattern.

....which is equivalent to "well, why wouldn't he design from a common pattern?"
LSS didn't say that verbatim, but that is what his response basically boils down to. You cannot assume that the designer would create de novo. Why are you assuming he would create de novo / why are you assuming he wouldn't create from a common pattern?

The question is not an assumption.
Now he is claiming that it is an argument from ignorance, as he says
”I can’t think of any good reason a designer would do it this way therefore a designer didn’t do it”. This is shoddy philosophy, this is not science.”
This does count as an an argument from ignorance fallacy - However - Jackson did NOT make that argument. So it is a straw man. The point was that Design doesn't have any expectations regarding the pattern, WHILE common descent does predict the pattern. HENCE, it is evidence for the latter and not for the former. That's the whole point of the very question: you cannot answer the question since design has no expected pattern. This is why LSS didn't answer the question - he couldn't. And he completely misunderstood what the question was about.
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7th: LSS is giving examples of patterns that are expected of Design....but not "ID" [3:05-4:29]
LSS objects to the argument that Intelligent design doesn't make any predictions regarding the pattern of organismal characteristics. It's not testable, it's ad hoc. He does this by, giving examples of:
- City researchers
- Archaeologists
- Cryptographers
- Forensic science

I am dumfounded...he has to be joking...there is just no way....it's the most absurd equivocation fallacy I have ever seen. We are in a disagreement on "intelligent design" and I am pretty that both sides are fully aware of that the point of disagreement is on whether complex life forms are the product of intelligent design or not. When we contest "intelligent design", we obviously aren't arguing whether things like the pyramids of Giza are the product of design. Likewise when Jackson said:
“design doesn’t make any predictions
He wasn't talking about "design" in general like. It was in relation to the subject being discussed before and after the statement - the appearance of traits in the history of life. This context so obvious, it shouldn't have to be re-stated. Is he being deliberately obtuse or is he just that dense, or it is some absurd combination? Only God knows. Just assuming that he is actually serious: No LSS, we aren't saying that the examples you gave make no predictions and aren't untestable. We contest ID by the fact that it - REGARDING BIOLOGY - does not make predictions and isn't testable. Any observation, again - REGARDING BIOLOGY - just in case you didn't lost the context, can be explained away by saying:
Well, the designer just wanted it to be that way for some reason.
If you disagree with that, don't equivocate "intelligent design" with all these other things, as if that would answer the question.

At the end he references Stephen Meyers as "making predictions". It would be better if he just skipped that part about "forensic science" and such and instead gave these predictions from Meyer instead. However, I watched the video he referenced. Meyers talks about "Junk DNA" and how it is "NOT JUNK!!", but he doesn't explain HOW "Intelligent Design" predicts that. From what mechanism of design do they argue, which restricts the genome from being overrun by Junk DNA? Or in other words: Isn't Meyers making a mere psychological objection? Isn't his argument that the designer WOULD not include junk DNA in the genome a faulty assumption? See what I did there? Meyers doesn't explain why he would expect this. He simply says (paraphrased) "Well, the Neodarwinists expected the DNA to be mostly Junk, so we predicted that Neodarwinists are wrong!" Which isn't a prediction that would support "intelligent design". The best arguments that ID proponents have is trying to poke holes into evolution and then proclaim victory by default. Intelligent design doesn't stand on its own merits, but evolution does. This is why they spend (almost exclusively) all of their time trying to discredit what they see as "the only alternative to theirs" - instead of giving substance to their own position. Evolution has substance that they can complain about non-stop, but ID has no substance. If you forced them to talk about ID without any reference to "alternatives", it would look like this:

And not just that, if there is no junk DNA, it wouldn't disprove evolution - specifically (rather ironically) "Neodarwinism" in the ACTUAL sense (meaning: natural selection + mendelian genetics). If the Darwinian mechanisms of natural selection are the only mechanisms that shape the genome, then everything that we see in the genome is the product of selection, i.e. functional. HOWEVER, junk DNA, the accumulation of non-functional DNA, is a product of Genetic Drift. It's an example of a NON-DARWINIAN evolution, nor "neodarwinism". That's why there are "evolutionists" who don't think that Junk DNA is real. Mostly the older ones.

But even so, Junk DNA is still a thing. I talked about it here. Or watch this lecture by PZ Myers

Skip to 40:38 for the conclusion.


8th: The platypus is "just" a monotreme...nothing more...oh the jargon [4:29-5:26]
He plays a clip of Jackson saying
The platypus is not a mosaic, it's a mammal, specifically a monotreme
And then goes on a tangent about how simply saying "monotreme" wasn't an answer. It's just technical jargon to make it appear like an answer was given. Except for the fact that this wasn't the whole answer - Jackson CONTINUES on explaining WHY the platypus is not a mosaic. In fact LSS later addresses that (tries to at least), so he knows that he gave a longer answer. Why wasting your time to go on a rant about how just saying "it's a monotreme" is a non-answer? (rhetorical question)

9th: Okay...I give up on my bad argument...but ONLY if you do the same with your good argument!! [5:26-6:00]
LSS says that Jackson argues that the platypus is not a mosaic, because
It's similarities [with distantly related organisms that LSS pointed to] are merely superficial
This is untrue. While some similarities that he pointed to were INDEED superficial. As explained, the structure of the electroreceptors have more in common with that of mammalian sweat glands, rather than the electroreceptors of fish. While other similarities that LSS pointed to actually make perfect sense for a mammal, when you understand their evolutionary history (which of course he doesn't). Such as:
1. Mammalian fur...well duh.
2. Laying (soft)shelled eggs, which is an ancestral characteristic of amniotes (mammals are included in that catagory).
3. The heel spur, which is an ancestral trait of Mammaliaformes.

So LSS again doesn't appear to understand the answer that was given to him. Which to me doesn't come to a surprise at this point. Furthermore, he goes on making an absurd argument. He is pleading for a false compromise. He will "give up on" the similarities of the platypus on the condition that we do the same for the “many of the most common putative homologies”. He insists that if we were being consistent with our reasoning, we would dismiss these homologies in the same way we dismissed the similarities of the platypus.

Of course, this simply doesn't work like that. We haven't just asserted that the platypus' similariteis are superficial - like he did with homologies. We provided detailed explanations for why - SOME of - the similarities were superficial, while he has done bupkis on his side of the argument. He hasn't even given a specific example of a "putative homology" which he regards as superficial. That's somehow LESS than nothing. We really don't have anything to respond to.

For there to be some consistency between us, LSS, you would have to provide one example of a "common putative homology" and provide an explanation for why it is superficial. I suggest starting with the tetrapod limb.
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9th: I agree with NCSE....or do I? [6:00-6:41]
Here LSS says that he agrees with the NCSE and that homology isn't evidence for common descent, it's just a label that is applied afterwards. But that's not the position of NCSE and he misses the point completely - again.

When NCSE says "homology is not "evidence" for common ancestry" in this paragraph: [notice the " " on "evidence"]
Screen Shot 2020-03-10 at 23.27.53.png
They mean it isn't evidence when it is used in the following form:
1. Assert that traits X Y and Z are homologous.
2. Homologous traits are the result of common descent
2. Therefore, common descent.
Which would be circular.

But they actually DO say that Homology is evidence for common descent. Hence the " " in the highlighted sentence above.
WHEN you use it in a non-circular way, as NCSE explains here:
Screen Shot 2020-03-10 at 23.33.38.png

When you properly use homology in reference to external evidence, as in the following:
1. The pattern of traits shared between species follows a nested hierarchy.
2. This is expected if species share a series of common ancestors
3. When we look more closely, we see the same thing again and again, even in embryology and genetics.
4. Hence more support common descent.
It is isn't circular and THAT is (in a grossly summarised nutshell) what is referred to when we say "homology is evidence of common descent".

9th: More on TalkOrigins....I have said this all along!! [6:41-7:44]
He claims that his reason for including that one line from the TalkOrigins page, is because he likes to include the best objection so people can see both sides of the argument. If that is the case, why did you only quote the first sentence. Why not the whole page? Why do you have to rip it out of the context like that, such that people couldn't see what the side of TalkOrigins was actually talking about? Your actions and the reasoning behind them are in stark contradiction.

And again, LSS thinks that the first sentence was meant to say argue that literally (non-hyperbolically) NOBODY would make the mistake of framing homology in a circular manner. When you include the context (you know the REST of the page), that first line was obviously in regard to the field of evolutionary biology and how the biologists discuss homology (not on behalf of literally everyone). As in:

[First line] = This isn't how biologists argue from homology as evidence for common descent
[The rest] = Rather this is how biologists argue from homology as evidence for common descent

Which makes the first line entirely reasonable. This is why LSS should have included "THE REST" when referencing this article, such that the context of the first line is clear. And since LSS now says he agrees with the rest of the page, he has no justifiable reason to make the same objection against the TalkOrigins page, unless of course he keeps ripping the first sentence out of context and present it as if it means "LITERALLY NOBODY MAKES THIS MISTAKE".

He has now admitted that homology can be used in a noncircular manner to support evolution when it references independent evidence...which we have pointed out to him...but here he acts as if this was he was saying all this time. Well, no...when you watch his first video (particularly the first half on homology before he goes onto phylogenetics) his argument is constantly.
Homology as evidence of common descent is circular. Homology as evidence of common descent is circular. Homology as evidence of common descent is circular. Homology as evidence of common descent is circular.
Nowhere in the video did he say something like:
However, even though it is often used in a circular way, homology can be used in a non-circular way, just like TalkOrigins explains it here. It relies on independent evidence. And This is perfectly acceptable
Acting as if you have been saying this from the get go is just a blatant way of avoiding to correct your mistakes.

Lastly, he contests whether the external evidence that supports the "homology is evidence claim" is any good. He of course argues that he has shown that this external evidence
1. The nested hierarchy
2. Phylogenetics
Are no good, but I have already covered those again and again, so we haven't missed any of it.

10th: Straw man, that wasn't the objection[7:44-8:10]
Jackson objected to him claiming that
"more and more people (present tense) are objecting to this use of homology"
in reference to decades old papers.

LSS has first responded with a "Huh"
Now LSS says that since the objections are old that doesn't mean they are wrong. That is correct, but that was NOT the objection. Jackson objected to you making this claim in such a way that makes it sound as if it refers to something fairly recent, which it wasn't. Jackson didn't say, they are old therefore they are wrong.


11th: The quotes....again... [8:10-9:40]
We have pointed out that the authors he quoted from in order to support his simplistic way of dismissing homology as a circular argument for evolution.

He objects to that by saying that
Quoting from someone with a bias against your own position has more weight than quoting someone with a bias for it,
This is true, however, Jackson didn't brought up the fact that since the authors believe that homology is still evidence of evolution, it meant that their objections to the modern definition of homology - that LSS highlighted - are invalid. It was to point out the nuance that LSS missed. As noted before, LSS argued in his original video that homology as evidence for evolution is circular and that's it. Nowhere in that video did he acknowledged that it - as it is properly understood by biologists - can be used in a non circular way. LSS referenced these authors to support this position, but they didn't argue for this position. That's why Jackson pointed out that the arguments were much more nuanced compared to his, such that they did not reject homology as evidence for common descent in the same way that LSS did. That was the point.

It's also telling that LSS simply dismisses the authors when they clearly state that homology is still supportive of evolution, as if they were like a mother trying to make excuses for his violent son who is on trial for murder. He doesn't give any ACTUAL reason for why he thinks they are "merely making excuses to explain away the problem". When you read the articles, they clear don't. They give reasons for why they think the homology label shouldn't be defined in evolutionary terms, but this has ultimately no bearing on whether it (the morphological traits themselves, not the label) is real evidence for evolution. So there was no "problem" that they had to "explain away".

And the definition of the label is irrelevant, since LSS has now agreed that you can use homology (even by that definition) as evidence of common descent when you reference independent evidence.

In fact, in the next point, LSS agrees that you can also avoid the circularity by defining "homology" in a pre-darwinian sense and use it as evidence for common descent....which is EXACTLY the position of the authors, who LSS previously dismissed as "merely making excuses to explain away the problem". Go figure.

12th: Again admitting that Homology isn't necessarily circular... [9:40-10:04]
So yeah, as said previously, here he is admitting that homology isn't always circular. That's the point we have brought up to him, but he acts as if WE are the ones misunderstanding him since HE supposedly was the one who was making this point from the start. That homology isn't always constructed in a circular way, it's just often is.

But again, when watching the original video, NOWHERE did he acknowledge that homology isn't always circular. And when you watch Jacksons first rebuttal, HE was the one who did acknowledge that homology is - unfortunately - often constructed in a circular way, but pointed out that it can be done such that it avoids the circularity. So LSS is just trying to steal the credit for this point...for some reason.

I can already expect that LSS will fall back to "well, homology (as defined in evolutionary terms) as evidence for evolution is circular", but here is the thing. We determine homology (in the evolutionary sense) by using the same methods to diagnose the homologies (in a pre-darwinian sense). When the pattern of these traits follow a nested hierarchy, we conclude that it is homologous in the evolutionary sense. This still isn't circular.

It all comes down to what we actually mean by “homologies are evidence of evolution”
LSS might think it goes like this:
“These 2 traits in these 2 species are homologous, they were inherited from a common ancestor.”
“How do you know they’re homologous?”
“Because these two organisms shared a common ancestor.”
“How do you know they shared a common ancestor?”
“Because these 2 traits are homologous, which means they were inherited from a common ancestor.” and round and round it goes.

But it actually goes more like this:
“These 2 traits in these 2 species appear morphologically and developmentally similar, and are present in two species for which we have sets of fossils that form a nested hierarchy, showing a gradual divergence of this trait from an intermediate trait, therefore I will call these traits homologous, which means they were inherited from a common ancestor.”
“How do you know they’re homologous?”
“Because of the data I just described.”
“How do you know they shared a common ancestor?”
“Because of the data I just described.”

13th: Reciprocal illumination... [10:04-10:24]
Yeah, he did fall back to that same argument...even though he previously admitted that it isn't circular IF you reference independent evidence. That is what Hennig's "reciprocal illumination" is all about. Testing data against theory, updating theory, and testing new data against this updated theory, which is the bedrock of all science. The independent evidence that shows the structures are "homologous" in the evolutionary sense. HENCE it is not circular, as LSS has admitted.

14th: The only error he admits...but denies the implications [10:24-10:53]
LSS doesn't agree with Jackson saying that it is apparent that LSS hasn't read his own citations. This is obvious. You have not read your own citations. The fact that you missed such an easily noticeable mistake, which is hard to miss when you read it even at a glance, is just one example that strongly indicates you haven't read them. Of course, this doesn't absolutely proof that you haven't read them, but still. It's difficult to see how anyone could miss a mistake like that when it is clear from just reading the caption of the figure alone.
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15th: More Straw manning [10:53-11:44]
Here Jackson explains why the discordant tree based on the cytochrome B data does not actually pose a problem. However, LSS cuts him off before he could explain it in full and summarises his argument as such:
Jackson basically says there are lot's of possible trees, so it is no big deal, so it is hard to find the right one

I am sorry LSS, that is NOT what he said: Here is what he ACTUALLY said, emphasis mine:
However, when we look up the original 1998 paper by Andrews et al, from which the weird primate tree based on cytochrome b claim comes from, we can see the figure that includes the statistical certainty for each branch. This is the maximum likelihood tree based on 10 mammalian cytochrome B nucleotide sequences. Some branches show high certainty, such as the one given for humans, colobus monkeys and squirrel monkeys has a near 100% likelihood, and the one for the bushbaby and loris has a 84.9% likelihood. Both of these relationships match the accepted phylogeny. However, for the other relationships that deviate from this, their certainties are rather low, lower than 25%. Meaning, these deviations from the accepted phylogeny are not well supported. Furthermore, this tree was just the one with the maximum likelihood, meaning the branching order of this particular tree gives the highest average likelihood among all possible trees that can account for the data that was used. Bear in mind that with even just 10 species, there are over 34 million possible trees you can construct, so finding the correct one isn’t easy to say the least. But that’s not all. Even if you determined the maximum likelihood tree, there often are still other possible trees with only a slightly lower likelihood. And indeed, Andrew et al found 1,731 other trees for which the likelihoods aren’t significantly different from that of the maximum likelihood tree, and these trees include the accepted phylogeny for these 10 mammals. In other words, the data from cytochrome b does not significantly support this discordant tree that LSS referenced in favor of the accepted phylogeny for these 10 mammals. For these and other reasons, Andrew et al concluded: “Only two groupings of species are clearly resolved by the cytochrome b data. These are the simian primates (Homo sapiens, Colobus guereza and Saimiri sciureus) and the lorisoid strepsirhine primates (Nycticebus coucang and Galago crassicaudatus). The branching order of the other taxa, including Tarsius bancanus and Lemurcatta, cannot be determined from the data.” Once again, completely refuting the claim that all genes should always show the same tree and it blows the cytochrome b argument completely out of the water

To summarise, the point (among others) is that the statistical support for this discordant tree is not statistically favoured over the accepted phylogeny. Basically, if the accepted phylogeny is the Null hypothesis and the discordant tree was a competing hypothesis, then the results points to the following conclusion: The support of the alternative hypothesis is not statistically significant - null hypothesis (i.e. accepted phylogeny) is not rejected in favour of the alternative hypothesis.

Or in other words: the cytochrome data does not contradict the accepted phylogeny, because using this data isn't enough resolve these topologies, as indicated by the statistics.

LSS doesn't take the statistical methods into account. He thinks that is it all about just finding one tree and that it is assumed to fit one tree- whatever works right? Wrong. These statistical methods are there BECAUSE we are trying to figure what the data shows. If you used a randomised data set. The method would show that all possible trees are equally supported. I.e. it doesn't fit any tree. However, here it shows that the data supported 1,731 different topologies with little differences between them regarding the significance. Recall that this is out of 34+ million (a fraction of less than 0.00006%). This is a very different story all together. The data overwhelmingly supports a tiny fraction of all the possibilities, a clear phylogenetic signal. Also note that the relationships within the incongruent trees that agree with the accepted phylogeny ARE well-supported, but the ones that deviate from the accepted phylogeny are not well-supported. So, it is not enough to resolve all of the topologies (as was explained), but it is far from just a random guess like LSS thinks it is.

LSS then cites more new articles. By Woese and Bapteste et al.
This is similarly about Horizontal gene Transfer, which is true and already addressed previously in point in the 4th point.

16th: Who is misunderstand who? [11:44-12:21]
LSS is completely clueless here.

He misunderstands Jackson as if he was saying:
LSS expects all genes to support the same tree
While he was saying:
LSS expects all genes to support the same tree IF DARWINISM IS TRUE

Jackson explained painstakingly why we do not expect what LSS is expecting from Darwinism. LSS completely missed this point (deja vu), he thought that Jackson was ascribing this expectation to him. And LSS continues on as if these are still the "expectations of the evolutionists".

Regarding the cytochrome B example, Jackson explained some of the basics of how phylogenetic analyses are done (which LSS clearly knows nothing about). He showed that the analysis concluded that the data does not statistically favour the discordant tree over the accepted phylogeny. BOTH are among the 1,731 different topologies (among +34 million) that were statistically significant supported by the data. Hence, it not only shows that LSS is wrong about his expectations from "Darwinism" - being based on his ignorance on how phylogenetic analyses are actually done, it also blows the cytochrome b argument out of the water.

Furthermore, LSS completely ignored the section from 16:10-18:20 of Jackson's last response. It's very important since it specifically addresses the main point that LSS is struggling with, i.e. his wrong headed expectation about "darwinism".

17th: Why not end with a Tu Quoque? [12:21-END]
Yes, the dover trial did indeed expose the Discovery Institute as motivated by a religious agenda. LSS of course has no answer to that. He said he will do a video on that some day. What a train wreck that will be, I have no doubt.

He asserts that the dover trial is actually embarrassingly for our case - somehow? When exactly?
That it was established that by the usual definition of "scientific theory" ID is not a scientific theory. And the according to Michael Behe's looser criteria - one that allows ID to be a scientific theory - would also allow astrology as a scientific theory? That's embarrassing for ID, not for us.

And at the end, he talks about how the NCSE and TalkOrigins have "prior commitments to atheism and naturalism". His way of saying "OH, the discovery institute are secretly creationist, well NCSE and TalkOrg are all secretly atheists!!" However, he doesn't know that they include members that are religious themselves. Just because they support science, specifically evolution, that doesn't mean they are atheists or (philosophical) naturalists. That's the first foundational falsehood of creationism.

And yes, there are prominent "non-creationist" on the Discovery Institute, such Michael Behe who accepts common descent, but even so, we have the wedge document form the discovery institute that shows their agenda as an organisation.

Not to mention that their banner has - ironically - evolved quite a bit over time.
THIS was the original banner of the Discovery Institute from 1996 to 1999.


And at the time, the Discovery Institute's president, Bruce Chapman, explained that the Center seeks
"To replace materialistic explanations with the theistic understanding that nature and human beings are created by God."

We have nothing of the sort for NCSE or TalkOrg. LSS is constructing a false equivalence.


Finally done. This has been an ordeal to finish.
If LSS wants to discuss these points - one by one - he is free to do so here on the League of Reason forum.
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Jackson published a new response video...in case you don't want to read everything I wrote here...this is a good summary.

Call Me Emo

New Member
This is why any fictional creature humans have imagined will almost always violate phylogeny - like the pegasus.

That's the same thing I try to explain to Creationists all the time. But because they don't understand the significance of Phylogenies, they don't understand the significance of the argument. 1mImageHandlerA (10).png
7mImageHandlerA (10).png


And another one...

This one is about another video LSS made for the Discovery Institute. The title is pretty self-explanatory.