Unfalsifiable Phylogeny

[Rumraket]

Repeat this simple statement until it sinks in: The total number of possible trees to construct from a limited set of sequences increases exponentially with the number of individual taxons.

Again, asserting that because it's "possible" for other trees to exist, means that they should exist if Common Descent is false.

It's a probabilistic argument, which you keep showing signs of not understanding. The argument isn't "it's possible - therefore it should". I've already told you that you can rationalize any concievable pattern by simply postulating "that's what the designer wanted". The problem is you don't have any fucking reason to expect the observed pattern on a design hypothesis over any OTHER concievable pattern.

Oh yeah, and this small thing here that YOUR DESIGNER HAS NEVER BEEN OBSERVED. (He also seemed wanting to design his creations in MATCHING TEMPORAL ORDER in the fossil record). Creation over billions of years, to make it look EVEN MORE like evolution did it.

In contrast, evolution predicts ONLY patterns like the one observed. And we have SEEN ALL THE MECHANISMS OF EVOLUTION.

Therefore, probabilistically, since no particular pattern is expected on design, but the one observed is expected on evolution, it's simply statistically much more likely.

There are no constraints on the design hypothesis. It predicts nothing. No observation could falsify it. It is a useless model.

You take ten loci in one species, say, Homo Sapiens, then you take the ten orthologous loci in Mice, then you take the ten orthologous loci in Cows, then you take the ten orthologous loci in however many species you want. Then you construct a phylogenetic tree for every single one of those ten loci, using the orthologous sequence from all the individual species.

What do you discover? Well shit buddy, they all fucking converge on the same statistical trend, rodents will group together, great apes will group together, bovines will group together, these will all further group together under mammals. Mammals will group with other vertebrates to the exclusion of molluscs, but both will grpup under animalia etc. etc.

And this is despite it being possible to construct UNTOLD QUINTILLIONS of trees from the dataset. Therefore, the theoretical total of divergent trees could outnumber the congruent tress to such an overwhelming degree, there is no expectation to see the convergence we do on probability alone.

There's only one explanation that makes sense and works only with observed mechanisms, that's evolution.

The foundation of your whole argument here is illusory. We find a dominant statistical pattern of similarities and differences (from an orthologous dataset ,selected because it is commonly shared) and, like a magician's trick, you automatically claim the mere existence of this pattern is evidence of Common Descent and hope nobody notices.

What are you even talking about? I've explained in exquisite detail why the observed pattern is a prediction of common descent, but not expected over any other concievable pattern on blanket design.

And no, the "re-uses old designs" retort still doesn't make sense for reasons already elaborated upon. For example, there would be no reason to re-design transcription factors, they could simply be kept constant. There'd be no reason to fill up the genomes of living organisms with degrading, inactivated pseudogenes. Or how about thousands upon thousands of retrotranspositionally inserting copies of degrading reverse-transcriptase genes? Just what the FUCK is the purpose if that, if you don't mind me asking? Did the designer WANT it to look like evolution happened?

How come we can do ANCESTRAL SEQUENCE RECONSTRUCTION using the same statistical methods we use to construct phylogenetic trees, RESURRECT ancient protein-coding gene-sequences and get ANCIENT FUNCTIONAL ENZYMES WITH A HIGH DEGREE OF SUBSTRATE PROMISCUITY?

How the fuck would that work on your design hypothesis? We collect the orthologues sequence from multiple species, using known mechanisms of mutation and population genetics, calculate the MOST PROBABLE ANCESTRAL SEQUENCE and splice it into a living bacterium. And what do we get? An entirely different enzyme with a different function.

If common descent wasn't true, there would simply be NO good reason to expect this possibility. You'd have to postulate that protein sequence space just so happens to be REPLETE with functional enzymes. What most creationists curiously insist it isn't, when they claim endlessly that almost all mutations are "loss of function" or "loss of information" mutations that almost always inevitably break protein function.

Make SENSE of it please.

Here are a few selected publications for you to rationalize away:
http://www.pnas.org/content/early/2013/06/12/1308215110.abstract
Experimental evidence for the thermophilicity of ancestral life

Abstract
Theoretical studies have focused on the environmental temperature of the universal common ancestor of life with conflicting conclusions. Here we provide experimental support for the existence of a thermophilic universal common ancestor. We present the thermal stabilities and catalytic efficiencies of nucleoside diphosphate kinases (NDK), designed using the information contained in predictive phylogenetic trees, that seem to represent the last common ancestors of Archaea and of Bacteria. These enzymes display extreme thermal stabilities, suggesting thermophilic ancestries for Archaea and Bacteria. The results are robust to the uncertainties associated with the sequence predictions and to the tree topologies used to infer the ancestral sequences. Moreover, mutagenesis experiments suggest that the universal ancestor also possessed a very thermostable NDK. Because, as we show, the stability of an NDK is directly related to the environmental temperature of its host organism, our results indicate that the last common ancestor of extant life was a thermophile that flourished at a very high temperature.

Oh look, they resurrect a 3.5 billion year old enzyme using orthologous sequences spread out over many Archaeal and Bacterial lineages, statistically inferred the ancestral sequence from which they all evolved. Reconstructed the protein sequence and spliced it into a bacteria which then proceeded to express it. They then purified the enzyme and tested it's properties. Turns out it worked extremely well and was highly thermostable. This is despite almost the entire amino acid sequence of the protein being different from it's extant descendants.

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001446
Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication

Abstract

Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.

Here's a nice subject overview:
http://pages.uoregon.edu/joet/thornton-NRG-2004.pdf
RESURRECTING ANCIENT GENES: EXPERIMENTAL ANALYSIS OF EXTINCT MOLECULES

Joseph W. Thornton
There are few molecular fossils: with the rare exception of DNA fragments preserved in amber, ice or peat, no physical remnants preserve the intermediate forms that existed during the evolution of today’s genes. But ancient genes can now be reconstructed, expressed and functionally characterized, thanks to improved techniques for inferring and synthesizing ancestral sequences. This approach, known as ‘ancestral gene resurrection’, offers a powerful new way to empirically
test hypotheses about the function of genes from the deep evolutionary past.

Why? Because Rumraket and Douglas Theobald assert it should be different if a designer did it.

No, because no other singular hypothesis fully explains all the properties of the dataset complete with predictive and explanatory power.

You have not elucidated any scientific reason why we should expect similar types of animals to group chaotically if Common Descent is false.

I'm not talking about similar types of animals. I'm talking about the gene sequences OF ALL LIFE. ALL their gene sequences, even those which are NOT physiologically constrained. Like enhancer and promotor regions. And then there's all the pseudogenes and ERV insertions. Just what the fuck is the purpose of all those degrading reverse-transcriptase genes again? Why do the mutations they accumulate ALSO form a massively statistically supported nested hierarchy? Why would a designer-recreate a dead AND useless gene? Why would the designer just constantly re-create this gene in a species over and over again every time "he" made a new one, and then mutate it further?

Explain it.

From your Theobald quotes:

There is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry. Though this logic may seem quite reasonable initially, all of molecular biology refutes this "common sense" correlation. In general, similar DNA and biochemistry give similar morphology and function, but the converse is not true—similar morphology and function is not necessarily the result of similar DNA or biochemistry. The reason is easily understood once explained; many very different DNA sequences or biochemical structures can result in the same functions and the same morphologies.

Here we go again. Because it's 'possible' for similar morphology to be constructed differently on a molecular level, then that it means it *should* appear that way if Common Descent didn't happen.

No, not that it SHOULD, but that it would be MUCH MORE LIKELY.

Unadulterated Darwinian Mysticism at work here.

It really does say a lot that straightforward, logically valid probabilistic reasoning is "mysticism" in maginmandunnit-land.

As a close analogy, consider computer programs. Netscape works essentially the same on a Macintosh, an IBM, or a Unix machine, but the binary code for each program is quite different. Computer programs that perform the same functions can be written in most any computer language—Basic, Fortran, C, C++, Java, Pascal, etc. and identical programs can be compiled into binary code many different ways. Furthermore, even using the same computer language, there are many different ways to write any specific computer program, even using the same algorithms and subroutines. In the end, there is no reason to suspect that similar computer programs are written with similar code, based solely on the function of the program.

I design 3D artwork on computers. I have created thousands of unique models and painted textures. There are many different methods and styles in how a complex 3D object is modeled, how its UV's (or its skin) is laid out flat to be painted, and especially how it is textured in a painting program.

That's good mate. Show me your nested hierarchies.

Tell me, if you can take a thing from one of your designs and re-use it in another where it would work perfectly well too, would you then bother changing it? Would you do this EVERY TIME? (Those strange enhancer and promoter regions are back to haunt us here again).

Also, since many different biological structures can perform the same function, why would there be so many different versions? Why the hundreds of different eyes if just one works fine for most? If the same underlying genetical framework works just as well, why change it ever so slightly(as if by genetic drift) in a new lifeform?

Why all the silent or neutral changes that serve no purpose. Just what the fuck is the point of all the silent and neutral mutations which themselves fall into nested hierarchies? Was the designer TRYING to design an evolutionary pattern?

Yes, yes. You can keep rationalizing all of them "that's what the designer wanted". But so fucking many of them simply doesn't make sense. There'd be NO REASON to change them.

Despite the theoretically possible millions of different ways to design these objects, I have my own distinct style, which allows me to proceed quickly, efficiently, and I enjoy it. I am not concerned with suddenly doing things completely differently all of the sudden, in case someone comes along and baldly asserts that my artwork arose by a series culled accidents.

Ohh, quickly, efficiently and enjoyful. That's hilarious. Is your designer a human being? Is he constrained by time, a lack of resources, and subject to the boredom of mind and backstraining repetitive labor?

Let's see what you wrote about your designer:

Hi Engelbert,

Since I've already stated I'm not interested in attempting to advance new scientific models, I'll respond to you on a more personal spiritual level. If I were you, I would honestly consider the possibility that Common Descent is false. I would consider the possibility that different kinds of lifeforms, even in their simplest molecular parts, are far too magnificently and functionally complex to have originated via culled genetic accidents or blind forces of any kind. I would suggest that different kinds of life had a Creator.

The Bible says that God is known by all men through the Creation and Conscience. God is known by the things that are made, and the sense of right and wrong written in our hearts. If I were in your position, questioning how the natural world came to be, I would consider the possibility that you already know the answer to this in your heart, and to humbly ask God yourself for further confirmation.

So you have no intention of putting forward alternative models.

Oh wait, your alternative model is goddidit, as if a human being inadvertently making it look like evolution. That's just fucking brilliant dude.

In fact, this is a common pattern amongst nearly all human designers.[/b]

Yes, the re-using of previous designs as templates. It is not at all common that these designs then fall masstively statistically attested into nested hierarchies. This almost never appens. It CAN be designed on purpose, but this is actually quite rare.

Unless we specifically set out to keep doing things differently, or are unhappy with our current designs, we prefer to re-use what we consider to be elegant, efficient and functional designs over and over and over again.

I agree, then why the fuck didn't your designer do that. Why did he recreate useless and dead reverse-transcriptase genes over and over gain, and further mutate them every time?

Oh wait, lemme guess. He was "unhappy" with the previous version. Is that it? You know the mind of god now? Why does god's unhappiness with his designs mysterously fall into a nested hiearchy? That's just his "taste"? Oh look, "it's what the designer wanted". :lol:

Why would he create, then re-use dead and broken pseudogenes, but also mutate them even further, when it is known that those mutations are silent and/or neutral. I.e. they have no physiological, developmental or adaptive effect on the organism? What's the point? Is he TRYING to make it look like evolution happened?

Why would he create, then re-use but keep mutating enhancer and promotor regions, when it is known that those mutations are silent and/or neutral. I.e. they have no physiological, developmental or adaptive effect on the organism? What's the point? Is he TRYING to make it look like evolution happened?

Why would he create, then re-use but keep mutating and changing transcription factors, when it is known that those mutations are silent and/or neutral. I.e. they have no physiological, developmental or adaptive effect on the organism? What's the point? Is he TRYING to make it look like evolution happened?

Isn't it interesting that the Design argument you and Theobald are using goes against everything we know about observed Designers?

It doesn't. Human designs don't normally fall into nested hierarchies. And human beings certainly don't run around changing their designs for no reason just to produce nested hierarchies. They certainly don't clutter their designs with random junk and then keep copying that junk and mutating it.

If you've already designed a mechanism for switching transcription on and off. Why would you keep mutating elements of the switching mechanism every fucking time you made a new organism? What's the point? Are you TRYING to make a nested hierarchy on purpose?

If someone chooses to believe these absolutely magnificent designs of nature arose by accident, then they intensely desire to ignore the obvious and believe lies. Romans 1:20 continues to become more and more fulfilled with each advance in modern Biology.

For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made, even his eternal power and Godhead; so that they are without excuse:

Thank you for your preachy but irrelevant statement of faith in scripture. Allow me to translate it into picture form:

 

[Rumraket]

You know, I haven't even advanced a Designer model in this thread.

HA HA HA HA HA.

You've done NOTHING ELSE. All you've done is basically to rationalize away with references to what human designers would do. Re-using old designs out of ejoyment, speed and efficiency. You also mysteriously happen to know that your designer is god for some reason.

It does seem very strange to me that god is constrained by human concerns of time and efficiency. And then, not to forget, there's the "enjoyment" retort, to which you probably analogously think of god's "creativity". Oh, he just likes to change things up now and again, I know him, we're old buddies. Something like that, right?

All I've done is pointed out how flimsy and flawed your assumptions are of what Design would look like.

By postulating your own which is utterly idiotic to the n'th degree. To you, the "designs" of life imply your god. But the reasons you use for implying design in the first place are HUMAN CONSTRAINTS.

What's worse, they don't actually FIT. Because the very same rationalization you use to explain why there could be a nested hiearchy doesn't actually make sense becaus there'd be no reason to keep chaing so many thousands of orthologous loci.

So your mutually contradictory rationalizations (designs look like they were designed by a physically constrained designer, except that the designer isn't actually constrained by anything - but a supernatural omnipotent god of the christian bible).

So you're simply down to an empty rationalization. God designed everything according to his taste. He WANTED to design the genomes of living organisms such that all aspects of it look like it evolved by common descent. Because, you know, he was (not actually) constrained by time and resources, so the only rationalization left for you IS the one of taste.
God designed life to look like it evolved, because he enjoyed it.

Thank you for this most interesting exposition of religious lunacy.

It is extremely interesting that your alleged evidence for Common Descent relies so heavily on your metaphysical beliefs about the nature of supernatural designers.

Strangely enough, you're the one who has supplied all the rationalizations about what designers wanted to do. I've simply made a straightforward probabilistic argument. There are many more ways to do designs than to do nested hierarchies. We don't know the designer, so there's no reason to expect it would operate in ways we see fit. In this respect I have actually REFRAINED from making statements about what designers would do.

But YOU know it, you just KNOW the designer was re-using old designs and mysteriously chronically mutating them slightly, even though he didn't have to. So it just so happened to still produce nested hierarchies even when there'd be no need to.

So then we get to your great ambivalence. Refer to human-constrained designs, but then turn around and imply the designer is manifestly non-human.

Nothing about your position makes sense. It's ad-hoc rationalization all the way down. Nothing meaningfully can be predicted from it. You're only here to propagandize for doctrine, to do christian apologetics.

Hey! Where's your designer again? Why has the design-mechanism never been observed? Human beings most certainly don't have the knowledge to make and populate entire planetary biospheres. But we know of a mechanism that does, and it's not design. The observed pattern fits the mechanism.

 

[Rumraket]

No, I'm saying it would me much more probable than otherwise. What is it you don't understand about the total number of incongruent trees theoretically being able to completely overwhelm the congruent ones? But this is not what we see.

That's the same thing I just said, only dialed back a notch. You are asserting phylogeny should "probably" be a chaotic mess if Common Descent is false. Because it is "theoretically possible" to have numerous incongruent trees? I've given up on expecting you to give a scientific explanation for this.

I have given scientific reasons for this. Genetics is not constrained to match morphology, there'd be no reason to expect the designer to design nested hierarchies to begin with.

Even if you "re-use old designs" there'd be no reason to expect:

1. Mutations in the new copies of old designed orthologous loci when most of these are neutral or silent, I.e. not the result of physiological (design)constraints.

2. Dead and broken pseudogenes and ERV insertions getting copied, then mutated too.

3. That the number of mutations in the vast majority of these re-used old genes (orthologous loci) converge on the same statistical trend, particularly when they're not due to physiological constraint.

4. The types of mutations most frequently detected in the orthologous loci are the ones expected for known biochemical reasons. As in all the usual about transitions being more likely than transversions, duplications statistically more likely in regions with increased chance of unequal crossing over. Ask yourself, just why the fuck would the designer just so happen to design in duplicated and mutated copies of genes in regions where we already would most expect them for biomechanical reasons?
Just why the fuck would the designer just so happen to design in the types of mutations in his new orthologous loci, already mostly expected for biochemical reasons? It's almost like these genes weren't actually created, but originated through mutation.

5. Different rates of mutations in different lineages matching for well known physiological reasons. Some species have increased mutation rates compared to others for reasons already understood(generation time, population size, metabolism etc. etc.). Why would your designer just so happen to have increasingly mutationally diverged the genomes of the lineages which we have found out have higher mutation rates(and no, not through phylogenetic means, but actual direct empirical observation of every generation)? There would be no reason for your designer to do this other than as a matter of taste. "Oh, I'm going to re-use the designs from my previously created species, but this time I will put in a lot more mutations spread out over the genome in this new one. Oh, I'll also just so happen to give this species an increased mutation rate compared to others, so that it looks like it actually diverged more through the accumulation of mutations over evolutionary time."

How come we have good reasons to see the pattern that we do on common descent? How come only the mechanisms of evolution have been observed, but your mysterious designer working on a planetary scale in the deep geological past, has not? Why is this so hard for you to grasp? You keep ignoring this point.
Yes, all concievable observations are compatible with design, but only a very small subset are compatible with evolution. We only have direct empirical validation of one designer, human beings, and what we know of human beings is that they weren't around for most of evolutionary time, and we most certaintly don't have the power to design entire planetary biospheres into existence. In contrast, evolution has been observed.

You might just as well expect Star-trees with equidistant leaves between all the nodes. Such that, for example, the human cytochrome C sequence was 10 mutations different from the chimp one, but also 10 mutations distant from the mouse one, and 10 mutations different from the squid one and so on and so forth. There would, simply statistically, be many many more of these kinds of possible incongruent phylogenies.

You are seriously claiming that, absent of CD, molecular differences between a human and a chimpanzee should be no different than a human from a squid? So I was right. If Evolution is false, you demand we should find strange non-sensical relationships such as Whales grouped with Pine cones.

That is entirely possible for many loci, yes. You see, you're the one who seems to imply that your designer would be re-using older designs when designing new species in some strange morphochronological sequence that matches with the evolutionary history of life.
Meaning he supposedly designed single celled life like bacteria and archaea first.
Then he took those and derived single-celled eukaryotes like yeasts and microfungi of various sorts.
Then he took those and derived multicellular organisms like sponges and jellyfish.
Then he took those and derived molluscs like snails, worms and squid from them.
Then he took some of those and gave them the ability to make shells and hard body parts.
Then he took those and made all sorts of strange insect-like arthropods from them.
Then eventually he took some of his worm-like creatues and derived some fish-like organisms from them.
Then he took those and derived more copies but gave them bony skeletons and jaws.
And on and on it goes, the designer creating new organisms from old templates, in this strange morphological and chronological sequence.

This is what we observe in the fossil record, a slow increase in morphological complexity over the history of life(and molecular phylogenetics is remarkably congruent with this picture). But technically your designer could have done the opposite, designed the most complex organisms first - then made them ever simpler and simpler. This would have been totally incompatible with evolution, where for good statistical reasons, life would more likely have started very simple, then slowly evolved more complex over time.

Also there are many genes he derived he didn't even have to change, because they serve the same basic function. In that respect, yes, we might just as well expect large portions of core metabolic genes to show no particular distance relationship, not to mention many promoter and enhancer regions. It is entirely possible that key metabolic enzymes in something as physiologically distant as squid and humans could show the same distance relationship as between humans and chimps. Or in some cases even none at all. There are many genes and loci a designer would not have had to change, the same basic structure would work just fine. But they ARE changed for some reason, and those changes fall into nested hierarchies. And the changes in them are most often silent or nearly neutral. Weird I tell you, it's almost as if they simply changed due to mutations getting fixed in splitting populations by genetic drift over evolutionary time.

You're the one who postulates the idea that the designer is re-using old designs, remember? But now you're suddenly against the idea. Now suddenly, the designer shouldn't be re-using his old designs, he should be tweaking them slightly every time he creates a new species, even when there being no physiological reasons to do so.

And all this is before we consider all the reasons I gave above, including the possiblity of ancestral sequence reconstruction and so on. Isn't it weird how it doesn't ACTUALLY look like the designer created extant species X, then derived extant species Y from it, but more like he created some now extinct species Z - then independently derived X and Y from that one? Isn't it weird how we can use the same statistical methods of molecular phylogenetics to reconstruct parts of the genomes of these no longer existing ancestral species and find out how and that they work?

You're also implying that such highly consistent molecular patterns exists when such expected "distances" between lineages are regularly violated. So much so that many evolutionary biologists question whether or not a reliable "molecular clock" even exists from which to model by. Of course, as I mentioned earlier, these prolific violators are easily explained away as sequences having various fluctuating levels of conservation by selection. Yet another evolutionary model where both the presence and absence of a pattern is confirming evidence for evolution.

And here you're asking us to ignore the known physiological reasons for why some species and genes would have increased rates of mutation. It's okay that you haven't actually bothered to understand these things, it's not okay that you then use this ignorance as a basis to dismiss the subject.

Apparently it bothers you that there are actual, empirically testable answers to these issues. You seem wanting to insinuate that they're simply rationalizations. But varying mutation rates can be empirically tested and the physiological causes can be elucidated.

Another criticism you might launch is that something along the lines that "similar physiologies require similar DNA sequences", but there is simply no reason to suspect this, in fact we know this assertion is false. Many similar physiological factors have been found with very discordant underlying genetics, and the opposite, many dissimilar physiological features have been found to have quite similar underlying genetics.

There is also no reason to suspect that just because something is unrestricted, that it *must* be exploited, as you have been repeatedly asserting without explanation. As I clarified above, this alleged design behavior is often completely at odds with actually observed Designers.

I haven't even made this claim, in fact I've made the exact opposite. That when things AREN'T physiologically constrained, on YOUR rationalization there'd be NO reason to change them. Like the enhancer and promoter regions for example. Why change them? Why KEEP changing them ever so slightly every time a new species is created?

Apparently you don't even understand what you read here.

Anyway, moving on to your little Gish-gallop of handpicked citations you don't understand:

We also know that similar non-homologous physiological features in distant animal groups have similar genetics.

Bats and dolphins inherited the same underlying hearing-related genetic framework from a mammalian common ancestor. That genetic framework is related to hearing in all mammals. If the same underlying genetic framework is subjected to the same physical constraints and selective pressures, why would it then be a suprise to see them converge on similar physiological solutions?

Explain it to me in your own words.

We also know that, in any given species, on average 10-30% protein-coding orphan genes lack any signal of Common Descent whatsoever.

In insects and related arthropods (in large multecellular eukaryotes like humans and other primates, the number of ORFan genes is less than half of one percent. For understood reasons (they mainly emerge from junk-regions, by mechanisms also understood).

Insects and the like evolve much more quickly, among other reasons due to their much shorter generation times. The significance of which, if you had a clue, you would understand.

Two significant patterns (among many) that directly contradict evolutionary expectations. (and admitted so by evolutionary biologists)

Extracted directly out of your ass. Not expected =/= expected not to happen. There's a difference there.

Comically however, under your flimsy metaphysical framework, any and all data that does not constitute a statistical majority, (a pattern you baldly assert could not result from any other process than Common Descent) is immediately rendered irrelevant.

Why do you keep telling outright falsehoods and attributing statements to me I don't make? I keep saying any concievable dataset can be rationalized on a design-hypothesis. But that the particular one we have is vastly improbable, in addition to having untold millions of peculiarities that only evolution can make sense of. The only "explanation" for them on your design hypothesis is to just rationalize them as "what the designer wanted".

Yes, you can rationalize them, a designer could have wanted life to appear the way it does. But we still SEE evolution happening. While your mysterious invisible designer god who can apparently design entire biospheres, stays curiously hidden, having done all his work in the deep geological past.

Extraordinary claims require extraordinary evidence. You have nothing but rationalization.

 

[Rumraket]

If you think science doesn't have metaphysical and philosophical underpinnings, you're wrong. Some of the key elements that lie at the hart of the scientific methodology are things like Occam's Razor, which is, yes, a metaphysical proposition. The justification for it's use lies in the fact that it works, that science without Occam's Razor would be worthless. Any observation could be explained ad-hoc by reference to an inifnity of phenomenon-causing little fairies. The problem is, if you let go of Occam's Razor, you inadvertently lose the capability to do predictions.

I never said metaphysical thinking is a bad thing. But when a specific theory is sold to the public as something supported by undeniable, empirical, scientific fact, but in reality is actually heavily reliant on metaphysical assumptions, I believe that needs to be addressed.

You haven't showed that any of the underlying reasoning is invalid.

Another thing you don't seem to understand is probabilistic reasoning, which is closely related to Occam's Razor. Or how statistics is used when dealing with stochastic processes such as evolution. You seem entirely unable to grasp how single incongruent loci here and there cannot falsify the main theory of common descent when there are many many more congruent loci than incongruent ones. It can, in point of fact, be falsified, you just need huge amounts.

Huge amounts of incongruence can be explained away by huge amounts of incomplete lineage sorting. I've already demonstrated this.

"Huge amounts" =/= main pattern averaged over all shared orthologous loci. Seriously, pick up a fucking book on molecular phylogenetics.

Occam's razor? Bah, who needs it? No reason to prefer simpler explanations that only work with the observed. Extraordinary claims require mundane evidence, or none at all, ad-hoc rationalization is fine as long as it fits it's "evidence"(kinda hard for a rationalization not to, don't you think?).

You think the claim that a series of culled genetic accidents turned single celled organisms into humans who created the internet, is an invocation of Occam's Razor? Really?

Observed, demonstrably effective testable natural mechanism vs unobserved magical divine miracle machine. Observed mechanism wins. Sorry.

Someone who faithfully ascribes miraculous creative powers to culled genetic accidents

The irony is that you're the one ascribing the existence of all species to actual literal divine miracles.

I'm simply showing that the observed mechanism can be extended indefinitely. All observed genomic loci are within reachable mutational distances from oneaother over available evolutionary time. We can reconstruct ancestral states using statistics and show that and how they worked. We don't have to posit anything miraculous, yet here you are, doing just that. And you're accusing me of postulating "miraculous creative powers". :lol:

Talked to any snakes lately too?

 

[lifepsyop]

Again, asserting that because it's "possible" for other trees to exist, means that they should exist if Common Descent is false.

It's a probabilistic argument, which you keep showing signs of not understanding. The argument isn't "it's possible - therefore it should". I've already told you that you can rationalize any concievable pattern by simply postulating "that's what the designer wanted". The problem is you don't have any fucking reason to expect the observed pattern on a design hypothesis over any OTHER concievable pattern.

I've already presented very simple and rational reasons to expect such patterns in systematics. Similar phenotypes are built on similar genetics. And here comes the Rumraket-Theobald hand-waving "BUT THEY **COULD** BE BUILT ON DIFFERENT GENETICS!!!" You then begin ranting and protesting that a Designer should have designed differently because he is omnipotent and shouldn't have to worry about efficiency concerns, as you posted earlier.

Ohh, quickly, efficiently and enjoyful. That's hilarious. Is your designer a human being? Is he constrained by time, a lack of resources, and subject to the boredom of mind and backstraining repetitive labor?

You are quite obviously using religious arguments. And you are actually demanding that a Designer go out of his way to practice what humans would consider unintuitive design, just because it's "possible".

Likewise, I could turn and say to you, the Evolution of genes could have progressed in such a way that de novo origin of "orphans" occurred far more frequently, wiping out a considerable amount of phylogenetic signal. This explanation is already used. There is no barrier to this process happening in greater degrees and frequencies within your model. Evolution would "explain" the absence of the pattern you are ranting about being overwhelming statistical evidence for Common Descent.

This type of explanatory power is not evidence of a good scientific model, but a model that lacks falsifiability because it attempts to explain too much.

Oh yeah, and this small thing here that YOUR DESIGNER HAS NEVER BEEN OBSERVED. (He also seemed wanting to design his creations in MATCHING TEMPORAL ORDER in the fossil record). Creation over billions of years, to make it look EVEN MORE like evolution did it.

If the fossil record is anything, it is a dominant pattern of major types of lifeforms existing as distinct islands of morphospace, largely lacking in intermediate connections. The ambiguous collection of so-called "transitions" is laughable. Comically, evolutionists have been backed into the position of asserting that the transitional events between major body plans generally occurred too rapidly to be recorded with fossils.

And there is no "matching temporal order" of the fossil record. From a distance, there is only a vague sequence of the major types of life. Evolutionists capitalize on this clumsy ordering as an easy talking point to sell to the public, however when we take a closer look into the fossil record, often times we find anything but an evolutionary narrative playing out. This can result in sometimes quite humorous evolutionary explanations.

For example, evolutionists paint a poetic picture of reptiles gradually transitioning into small rat-like creatures as basal mammals: similar to reptiles, and only later in the evolution of mammals would we find the more "advanced" mammalian traits emerging, such as adaptations for air and water, and other features commonly associated with the "higher" mammals.

However, one of the "first mammals" in the fossil record is this critter.
Castorocauda

Castorocauda is a genus of small, semi-aquatic mammal relatives living in the Jurassic period, around 164 million years ago, found in lakebed sediments of the Daohugou Beds of Inner Mongolia. It contains the single species Castorocauda lutrasimilis. They were highly specialized, with adaptations evolved convergently with those of modern semi-aquatic mammals such as beavers, otters, and the platypus...

....The discovery of Castorocauda lutrasimilis is the first sign that a close relative of mammals adapted to water before dinosaurs lost dominance 65 million years ago, pushing back the estimated date for mammal relatives adapted to a semi-aquatic lifestyle by 110 million years.

....It provides the earliest absolutely certain evidence of hair and fur. Previously the earliest was Eomaia, a crown group mammal from about 125M years ago.

Perhaps the most comical assumption made is that this creature wasn't even a "true" mammal, but a relative of mammals that had "convergently evolved" all of these traits seen in otherwise advanced semi-aquatic mammals not found 100+ million years later! :lol:

Oh yes, the other animal "dated" to the same time period is what is essentially a flying squirrel.

Of course, the expected religiously infused response from any evolutionist is: So what? Natural Selection dunnit!

But the point is, again, how flimsy the case is for Common Descent, and how well-insulated it is from falsifiability. On any closer inspection of the fossil record, this seeming "matching temporal order" immediately breaks down, and we find a cascade of non-falsifiable explanations for why so many specimens appear to defy evolutionary narratives.

In contrast, evolution predicts ONLY patterns like the one observed. And we have SEEN ALL THE MECHANISMS OF EVOLUTION.

:roll: Vague and ambiguous equivocation.

Therefore, probabilistically, since no particular pattern is expected on design, but the one observed is expected on evolution, it's simply statistically much more likely.

Ridiculous. A pattern results from comparative studies on biology. You baldly assert it is an "evolutionary pattern"

Let's see how many patterns does Evolution "explain"?

Any pattern of shared genetic sequences can be "explained" by both common descent and convergent evolution.
Any pattern of shared phenotypic traits can be "explained" by both common descent and convergent evolution.
Any pattern of genetic sequences with no signal of common descent (Orphans) can be "explained" by "de novo" evolution.
Any pattern of phylogenetic discordance can be "explained" by incomplete lineage sorting.

There are no constraints on the design hypothesis. It predicts nothing. No observation could falsify it. It is a useless model.

Though I obviously believe in intelligent design, that is, the God of the Bible as Creator of all things as written in Genesis, I am not advancing a design hypothesis here. I'm simply investigating whether or not Evolution / Common Descent is a scientific or metaphysical model. Clearly, it is a metaphysical model lacking any robust criteria for falsifiability.

However, since you insist on derailing the thread, a design inference based on the Bible predicts many things. For one, that natural abiogenesis is impossible, as God is required for life. Oh, how easy it would have been to falsify the Bible if spontaneous generation turned out to be true (as many 'scientists' have believed and still believe). Likewise if, in the thousands of years of recorded history, mankind had ever observed and documented one distinct kind of animal giving birth to another distinct kind. Boom - instant falsification of the Bible.

 

[DutchLiam84]

You should write a paper highlighting every objection you have and submit it to a journal like Science or Nature, I think they would be happy to publish it if your case is valid. Just like the fact you've found objects (entire galaxies) that can move faster than the speed of light. You're on your way to a Nobel prize my friend, several in fact.

 

[lifepsyop]

And no, the "re-uses old designs" retort still doesn't make sense for reasons already elaborated upon. For example, there would be no reason to re-design transcription factors, they could simply be kept constant. There'd be no reason to fill up the genomes of living organisms with degrading, inactivated pseudogenes. Or how about thousands upon thousands of retrotranspositionally inserting copies of degrading reverse-transcriptase genes? Just what the FUCK is the purpose if that, if you don't mind me asking? Did the designer WANT it to look like evolution happened?

How come we can do ANCESTRAL SEQUENCE RECONSTRUCTION using the same statistical methods we use to construct phylogenetic trees, RESURRECT ancient protein-coding gene-sequences and get ANCIENT FUNCTIONAL ENZYMES WITH A HIGH DEGREE OF SUBSTRATE PROMISCUITY?

How the fuck would that work on your design hypothesis? We collect the orthologues sequence from multiple species, using known mechanisms of mutation and population genetics, calculate the MOST PROBABLE ANCESTRAL SEQUENCE and splice it into a living bacterium. And what do we get? An entirely different enzyme with a different function.

If common descent wasn't true, there would simply be NO good reason to expect this possibility. You'd have to postulate that protein sequence space just so happens to be REPLETE with functional enzymes. What most creationists curiously insist it isn't, when they claim endlessly that almost all mutations are "loss of function" or "loss of information" mutations that almost always inevitably break protein function.

Make SENSE of it please.

Here are a few selected publications for you to rationalize away:
http://www.pnas.org/content/early/2013/06/12/1308215110.abstract
Experimental evidence for the thermophilicity of ancestral life

Abstract
Theoretical studies have focused on the environmental temperature of the universal common ancestor of life with conflicting conclusions. Here we provide experimental support for the existence of a thermophilic universal common ancestor. We present the thermal stabilities and catalytic efficiencies of nucleoside diphosphate kinases (NDK), designed using the information contained in predictive phylogenetic trees, that seem to represent the last common ancestors of Archaea and of Bacteria. These enzymes display extreme thermal stabilities, suggesting thermophilic ancestries for Archaea and Bacteria. The results are robust to the uncertainties associated with the sequence predictions and to the tree topologies used to infer the ancestral sequences. Moreover, mutagenesis experiments suggest that the universal ancestor also possessed a very thermostable NDK. Because, as we show, the stability of an NDK is directly related to the environmental temperature of its host organism, our results indicate that the last common ancestor of extant life was a thermophile that flourished at a very high temperature.

Oh look, they resurrect a 3.5 billion year old enzyme using orthologous sequences spread out over many Archaeal and Bacterial lineages, statistically inferred the ancestral sequence from which they all evolved. Reconstructed the protein sequence and spliced it into a bacteria which then proceeded to express it. They then purified the enzyme and tested it's properties. Turns out it worked extremely well and was highly thermostable. This is despite almost the entire amino acid sequence of the protein being different from it's extant descendants.

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001446
Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication

Abstract

Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.

Here's a nice subject overview:
http://pages.uoregon.edu/joet/thornton-NRG-2004.pdf
RESURRECTING ANCIENT GENES: EXPERIMENTAL ANALYSIS OF EXTINCT MOLECULES

Joseph W. Thornton
There are few molecular fossils: with the rare exception of DNA fragments preserved in amber, ice or peat, no physical remnants preserve the intermediate forms that existed during the evolution of today’s genes. But ancient genes can now be reconstructed, expressed and functionally characterized, thanks to improved techniques for inferring and synthesizing ancestral sequences. This approach, known as ‘ancestral gene resurrection’, offers a powerful new way to empirically
test hypotheses about the function of genes from the deep evolutionary past.

With presentations like these, it's not hard to see how someone can be willingly fooled into believing the case for Evolution / Common Descent is stronger than it actually is. Use a science-y sounding phrase like "Ancestral Gene Resurrection", and insist that such data can only be explained by Evolution, and your average lay-reader will walk away believing there is a mountain of genetic evidence for Common Descent, when in actuality the whole argument is built on an illusion.

Here's an example of some of the resurrected "ancestors" from the last paper you linked.
http://pages.uoregon.edu/joet/thornton-NRG-2004.pdf

Digestive ribonucleases Ancestral orthologue in LCA of buffalo and ox
L1 retroposons in mouse Ancestral paralogue in mouse genome
Digestive ribonucleases Ancestral orthologue in LCA of artiodactyl
Chymase proteases Ancestral orthologue in LCA of mammals
Tc1/mariner transposons Ancestral paralogue in genomes of 8 salmonids
Immune RNases Ancestral orthologue in LCA of ‘higher primates’
Pax transcription factors Ancestral paralogue (older than the protostome–deuterostome ancestor)
Vertebrate rhodopsins Ancestral orthologue in LCA of archosaurs
Vertebrate short-wave rhodopsins Ancestral orthologue in LCA of bony vertebrates
Steroid hormone receptors Ancestral paralogue (older than the protostome–deuterostome ancestor)
Elongation factor EF-Tu Ancestral orthologue in LCA of eubacter

All that this shows is that certain traits are predictably expressed at certain genomic locations, some of which have been inactivated. For example, certain digestive enzymes are located in many or all ungulates, and some are no longer functioning. This is certainly not evidence that the enzyme originated from an evolutionary ancestor. The inference doesn't even depend on that.

This "phylogenetic inference" is the same as taking the genes controlling vision in other vertebrates to infer where those genes would be located in a vertebrate no longer expressing fully developed eyes. While this may seem silly because it seems obvious (even biochemically necessary) where the vision genes would be found in a vertebrate body plan, you are using the same reasoning with "ancestral gene resurrection": observing where a trait is expressed in one organism, to infer where it will be expressed in another.

I also like how the actual name of the methodology has the word "ancestor" in it, creating the illusion and implying such comparative inferences would be impossible without first accepting Common Descent.

You have not elucidated any scientific reason why we should expect similar types of animals to group chaotically if Common Descent is false.

I'm not talking about similar types of animals. I'm talking about the gene sequences OF ALL LIFE. ALL their gene sequences, even those which are NOT physiologically constrained. Like enhancer and promotor regions.

Evidence please. Please Demonstrate that any given enhancer/promoter region absolutely does not lend any amount of function to an organism, and never did in the past. How many times has this knee-jerk evolutionary assumption been proven wrong?

And then there's all the pseudogenes and ERV insertions. Just what the fuck is the purpose of all those degrading reverse-transcriptase genes again? Why do the mutations they accumulate ALSO form a massively statistically supported nested hierarchy?

I've already shown in the OP that ERV's contradict evolutionary narratives but are rescued with non-falsifiable explanatory devices.

A simple purpose of degrading material in a Creation could be punishment by the Creator for disobedience. A scenario like this is directly predicted in Genesis.

You have yet to support the nested hierarchy is evidence of Common Descent without religious/metaphysical argument dependencies. I am not here to argue against your religious beliefs.

Why would a designer-recreate a dead AND useless gene? Why would the designer just constantly re-create this gene in a species over and over again every time "he" made a new one, and then mutate it further?

Explain it.

Make an argument. "Mutate it further" ? Are you going to bluff with the molecular clock that doesn't exist again?

Is he TRYING to make it look like evolution happened?

If God had wanted to make it look like Evolution happened, He would have given you a viable mechanism for it. Culled genetic accidents as the mechanism producing all life on Earth, even a single complex anatomical feature such as feathers, is absolutely laughable. Running around hand-waving "Natural Selection dunnit, Natural Selection dunnit!" (and this *is* the obscurity that nearly every Evolutionary narrative boils down to) does not make your origins story particularly impressive.

Isn't it interesting that the Design argument you and Theobald are using goes against everything we know about observed Designers?

It doesn't. Human designs don't normally fall into nested hierarchies.

Human designs fall into nested hierarchies practically by definition, when creating variations upon a common underlying manufacturing theme. I am amazed at your willingness to obfuscate such a plainly obvious fact in order to defend Common Descent and compulsively deny the slightest bit of comfort to Design proponents.

Furthermore, the nested hierarchy observed in nature isn't even any kind of specific prediction of Evolution. Evolution could "explain" countless different nested hierarchies and arrangements by appealing to convergent evolution. (You yourself in the next post just stated it is expected to find convergent genetic sequences as well!)

For example, how many times have we heard that the fact that "mammals lack feathers" is evidence of an evolutionary nested hierarchy, (because feathers only nest within birds, which nest within reptiles, etc. ) Well guess what? In the evolutionary model, there is no barrier preventing mammals from "convergently evolving" feathers. If mammals had feathers it would not deter Evolution in the least, yet "mammals' lack of feathers" becomes evidence for the nested hierarchy of Evolution. Funny how that works, huh? A lot of illusion at work, and I hope readers are considering it.

 

[lifepsyop]

You should write a paper highlighting every objection you have and submit it to a journal like Science or Nature, I think they would be happy to publish it if your case is valid. Just like the fact you've found objects (entire galaxies) that can move faster than the speed of light. You're on your way to a Nobel prize my friend, several in fact.

Why would someone try to submit a paper questioning Common Descent to an Evolution journal?

That's like suggesting someone submit a paper proposing Common Descent to a YEC journal.

 

[he_who_is_nobody]

Why would someone try to submit a paper questioning Common Descent to an Evolution journal?

That's like suggesting someone submit a paper proposing Common Descent to a YEC journal.

:facepalm:

I see you are more then happy to display your ignorance of other subjects as well. There is so such thing as evolution journal, only scientific journals. Furthermore, there is no such thing as YEC journals, only propaganda mills that are more then happy to repeat long debunked myths about evolution/creationism.

However, admitting that your ideas would not be published in scientific journals and real science would not be published in YEC journals seems to be an exposer, on your part, of which ideas are based on reality and which are based on blind faith.

 

[DutchLiam84]

You should write a paper highlighting every objection you have and submit it to a journal like Science or Nature, I think they would be happy to publish it if your case is valid. Just like the fact you've found objects (entire galaxies) that can move faster than the speed of light. You're on your way to a Nobel prize my friend, several in fact.

Why would someone try to submit a paper questioning Common Descent to an Evolution journal?

That's like suggesting someone submit a paper proposing Common Descent to a YEC journal.

:lol: An Evolution journal? Dude, the ignorance is strong in you! The hell are you talking about? Even if Nature or Science was, like you call, an Evolution journal; why would it be impossible to submit a paper questioning anything. Do you have any idea how science works?

How the fuck would we ever progress in science if we were not able to question anything and everything? I myself am at the verge of publishing a paper questioning a 10 year old paper that has been cited over 100 times (I am a marine biologist btw). Just because you're paper goes against a certain paradigm doesn't mean you can't publish it, IF what you say is plausible. So I ask you the same question and please give an honest answer, don't ignorate (I'm coining this word) your way out of it. Let me make it more broad.

Why don't you submit a paper to ANY scientific journal (read scientific) with an impact factor of say 2.5 or higher? I dare you, no, I double dare you. I would even pay for possible publishing costs.

 

[ldmitruk]

You should write a paper highlighting every objection you have and submit it to a journal like Science or Nature, I think they would be happy to publish it if your case is valid. Just like the fact you've found objects (entire galaxies) that can move faster than the speed of light. You're on your way to a Nobel prize my friend, several in fact.

Why would someone try to submit a paper questioning Common Descent to an Evolution journal?

That's like suggesting someone submit a paper proposing Common Descent to a YEC journal.

:lol: An Evolution journal? Dude, the ignorance is strong in you! The hell are you talking about? Even if Nature or Science was, like you call, an Evolution journal; why would it be impossible to submit a paper questioning anything. Do you have any idea how science works?

How the fuck would we ever progress in science if we were not able to question anything and everything? I myself am at the verge of publishing a paper questioning a 10 year old paper that has been cited over 100 times (I am a marine biologist btw). Just because you're paper goes against a certain paradigm doesn't mean you can't publish it, IF what you say is plausible. So I ask you the same question and please give an honest answer, don't ignorate (I'm coining this word) your way out of it. Let me make it more broad.

Why don't you submit a paper to ANY scientific journal (read scientific) with an impact factor of say 2.5 or higher? I dare you, no, I double dare you. I would even pay for possible publishing costs.

I up your dare to triple dog dare. Bottom line is lifepsyop's idea of science is godditit and his idea of research is to cherry pick out of journals things he thinks support intelligent design. If he had a real case to bust the idea of common descent then why doesn't he show us some original research he has published. Oh, wait a minute IDiots don't do original research, silly me. :lol:

 

[Dave B.]

However, since you insist on derailing the thread, a design inference based on the Bible predicts many things. For one, that natural abiogenesis is impossible, as God is required for life. Oh, how easy it would have been to falsify the Bible if spontaneous generation turned out to be true (as many 'scientists' have believed and still believe). Likewise if, in the thousands of years of recorded history, mankind had ever observed and documented one distinct kind of animal giving birth to another distinct kind. Boom - instant falsification of the Bible.

First of all, spontaneous generation and abiogenesis are NOT the same thing no matter what creationists would have you believe. I believe you are aware of this but wish to argue against a straw man instead so I won't bother to explain the obvious differences.

Secondly, "one distinct kind of animal giving birth to another distinct kind" would actually falsify evolution. I'm sure the creationists would just claim this as a miracle and ignore it so there is no way this would falsify the bible.

 

[Dave B.]

You should write a paper highlighting every objection you have and submit it to a journal like Science or Nature, I think they would be happy to publish it if your case is valid. Just like the fact you've found objects (entire galaxies) that can move faster than the speed of light. You're on your way to a Nobel prize my friend, several in fact.

That's just it, though. Creationists seem to think there is this huge fucking conspiracy that is preventing them from getting their "science" into mainstream, peer-reviewed journals. According to them no one will listen because evolution has to be true and anything that contradicts the theory will be ignored.

I am a believer of evolution but I promise you that if I ever come across any research that would prove that the theory is incorrect I would submit that shit in a heart beat. I have no emotional attachment to the theory whatsoever. I would love nothing more than to prove that the theory of evolution is wrong.

(edited to correct punctuation)

 

[he_who_is_nobody]

I will leave the brunt of the work to Rumraket, but I thought I would chime in with a few things.

I've already presented very simple and rational reasons to expect such patterns in systematics. Similar phenotypes are built on similar genetics.

Tell that to wolves/thylacines and whales/hippos.

If the fossil record is anything, it is a dominant pattern of major types of lifeforms existing as distinct islands of morphospace, largely lacking in intermediate connections. The ambiguous collection of so-called "transitions" is laughable. Comically, evolutionists have been backed into the position of asserting that the transitional events between major body plans generally occurred too rapidly to be recorded with fossils.

And there is no "matching temporal order" of the fossil record. From a distance, there is only a vague sequence of the major types of life. Evolutionists capitalize on this clumsy ordering as an easy talking point to sell to the public, however when we take a closer look into the fossil record, often times we find anything but an evolutionary narrative playing out. This can result in sometimes quite humorous evolutionary explanations.

I could just leave that image to show how wrong you are, but I will point back to one of my post wherein I presented a wikipedia link (I guess it is okay to do that now) listing numerous transitional fossils in both temporal and morphologic order. This comment alone goes along way in displaying your understanding of the fossil record amounts to little more than what is found in a Prehistoric Playset. Your ignorance is not an argument.

For example, evolutionists paint a poetic picture of reptiles gradually transitioning into small rat-like creatures as basal mammals: similar to reptiles, and only later in the evolution of mammals would we find the more "advanced" mammalian traits emerging, such as adaptations for air and water, and other features commonly associated with the "higher" mammals.

However, one of the "first mammals" in the fossil record is this critter.
Castorocauda

Castorocauda is a genus of small, semi-aquatic mammal relatives living in the Jurassic period, around 164 million years ago, found in lakebed sediments of the Daohugou Beds of Inner Mongolia. It contains the single species Castorocauda lutrasimilis. They were highly specialized, with adaptations evolved convergently with those of modern semi-aquatic mammals such as beavers, otters, and the platypus...

....The discovery of Castorocauda lutrasimilis is the first sign that a close relative of mammals adapted to water before dinosaurs lost dominance 65 million years ago, pushing back the estimated date for mammal relatives adapted to a semi-aquatic lifestyle by 110 million years.

....It provides the earliest absolutely certain evidence of hair and fur. Previously the earliest was Eomaia, a crown group mammal from about 125M years ago.

Perhaps the most comical assumption made is that this creature wasn't even a "true" mammal, but a relative of mammals that had "convergently evolved" all of these traits seen in otherwise advanced semi-aquatic mammals not found 100+ million years later! :lol:

Oh yes, the other animal "dated" to the same time period is what is essentially a flying squirrel.

First off, after poking around a bit on wikipedia, I am not sure why exactly Castorocauda is referred to as a relative of mammals instead of a mammal. It appears to have the inner-ear bones that make mammals mammals. However, this is a nomenclature debate way outside of your knowledge base. You need to learn how to crawl before you try running a marathon.

Second, the poetic picture you are painting is ten to twenty years out of date. There have been several fossil discoveries that show there were several niches mammals exploited before the mass extinction 65 million years ago. I also do not see where you are going with this argument. Showing that mammals were more diverse before the K/Pg event only disproves old ideas in paleontology, not the theory of evolution. Please explain your thinking on this matter.

Furthermore, claiming Volaticotherium was essentially a flying squirrel further exposes your lack of knowledge about taxonomy, anatomy, and cladistics. In addition, both of these examples disprove your very first sentence as well. Have you ever heard of making an internally consistent argument?

However, since you insist on derailing the thread, a design inference based on the Bible predicts many things. For one, that natural abiogenesis is impossible, as God is required for life. Oh, how easy it would have been to falsify the Bible if spontaneous generation turned out to be true (as many 'scientists' have believed and still believe). Likewise if, in the thousands of years of recorded history, mankind had ever observed and documented one distinct kind of animal giving birth to another distinct kind. Boom - instant falsification of the Bible.

First off, you claim a god is required for life based on nothing, thus this claim can be dismissed. Second, natural abiogenesis appears to be more than possible; again, your ignorance is not an argument. Third, abiogenesis is not the same as spontaneous generation. Fourth, several theists also believed that spontaneous generation worked within a biblical view of the world. Fifth, define kind, in a meaningful way, and I will be more than happy to show you one kind “giving birth” to another kind.

Furthermore, you are the one derailing this thread. Rumraket has answered every challenge you made on this forum directly. You are the one that has doubled down either on your false claims or Gish Galloped to other claims, such as the comments I addressed above.

 

[Isotelus]

First off, after poking around a bit on wikipedia, I am not sure why exactly Castorocauda is referred to as a relative of mammals instead of a mammal. It appears to have the inner-ear bones that make mammals mammals. However, this is a nomenclature debate way outside of your knowledge base. You need to learn how to crawl before you try running a marathon.

Second, the poetic picture you are painting is ten to twenty years out of date. There have been several fossil discoveries that show there were several niches mammals exploited before the mass extinction 65 million years ago. I also do not see where you are going with this argument. Showing that mammals were more diverse before the K/Pg event only disproves old ideas in paleontology, not the theory of evolution. Please explain your thinking on this matter.

Furthermore, claiming Volaticotherium was essentially a flying squirrel further exposes your lack of knowledge about taxonomy, anatomy, and cladistics. In addition, both of these examples disprove your very first sentence as well. Have you ever heard of making an internally consistent argument?

The Wikipedia article doesn't go into enough detail, but I do have the paper. If you look at the figures, Castorocauda retains post-dentary bones, i.e. they are still associated with the dentary and have not migrated to the ear as would be the case in crown group mammals, hence the designation of C. lutrasimilus as a mammaliaform (lifepsyop's use of "true mammals" would allude to crown group mammals. I would advise against using this term again, because in cladistics true mammals refers to Eutheria). Hundreds of other characters nested C.lutrasimilus deeply within Docodonta, a group of mammialforms intermediate between the primitive Morganucodon and Sinoconodon and derived Hadrocodium, the latter of which is just outside of crown Mammalia. Some other primitive characters more obvious in the figure include a dorsoventrally flat skull that is posteriorly broad and a poorly defined lumbar region.

The important point here is that there are many mammalian groups including Docodonta that are separate lineages not directly ancestral to modern mammals. The specialized characters of Castorocauda are not associated with crown mammalian synapomorphies, and instead represent an independent "experiment", as it were, originating from the more basal Docodontan bauplan. This means that in spite of Castorocauda's specializations, it is still more primitive than any crown group mammal; even the earliest ones. The fact that Castorocauda represents an alternate branch, thereby demonstrating that there is no temporal discordance, renders lifepsyop's argument false and misguided. Additionally, as evolution is a non-linear process that does not necessarily occur at equal rates across time in groups or populations, the contemporaneity of derived and basal forms is entirely expected and well-documented both in the fossil record and in the present.
It is not clear why the third sentence about fur was highlighted. For future reference, it's old news that fur is symplesiomorphic for mammals, and as such is never used as a trait in determining mammalian relationships.

I wish I could respond to more, but I don't think I'll have much time.

 

[he_who_is_nobody]

First off, after poking around a bit on wikipedia, I am not sure why exactly Castorocauda is referred to as a relative of mammals instead of a mammal. It appears to have the inner-ear bones that make mammals mammals. However, this is a nomenclature debate way outside of your knowledge base. You need to learn how to crawl before you try running a marathon.

The Wikipedia article doesn't go into enough detail, but I do have the paper. If you look at the figures, Castorocauda retains post-dentary bones, i.e. they are still associated with the dentary and have not migrated to the ear as would be the case in crown group mammals, hence the designation of C. lutrasimilus as a mammaliaform (lifepsyop's use of "true mammals" would allude to crown group mammals.

Well damn, I was wrong about the inner-ear bones when it came to Castorocauda, thus wrong when calling it a mammal. It is times like this that I wish I still had my old university's access and not just wikipedia.

It is not clear why the third sentence about fur was highlighted. For future reference, it's old news that fur is symplesiomorphic for mammals, and as such is never used as a trait in determining mammalian relationships.

It is not obvious to you? It is because lifepsyop is vastly ignorant of the fossil record, especially the last decade or two of discoveries.

 

[Isotelus]

Well damn, I was wrong about the inner-ear bones when it came to Castorocauda, thus wrong when calling it a mammal. It is times like this that I wish I still had my old university's access and not just wikipedia.

No, not necessarily. There are a handful of researches who restrict mammals as we would think of them to crown group mammalia only, as was done to in this instance, while others identify it with the presence of dental occlusion and a dentary-squamosal jaw articulation, which Castorocauda and a few other more primitive examples have. It's not really that big of a distinction when it comes right down to it. In either case, as Castorocauda is not ancestral to modern mammals, it is wrong to call it a crown group mammal (what lifepsyop thought was a comical assumption but is actually extremely well-supported), i.e. a member of the group including all living taxa and the descendants of their most recent common ancestor.
In terms of discussing mammals vs. non-mammals by the second definition, it makes more sense to look at Morganucodon, because it has the derived dentary-squamosal jaw articulation and the primitive (albeit reduced) articular-quadrate jaw articulation.

It's times like this that I wish more journals were open access! Wikipedia and news articles are never as interesting or as informative as the original papers.

It is not obvious to you? It is because lifepsyop is vastly ignorant of the fossil record, especially the last decade or two of discoveries.

That yes, but what's not obvious is the relevance of the statement to his argument considering both of our comments on the subject.

 

[lifepsyop]

The important point here is that there are many mammalian groups including Docodonta that are separate lineages not directly ancestral to modern mammals. The specialized characters of Castorocauda are not associated with crown mammalian synapomorphies, and instead represent an independent "experiment", as it were, originating from the more basal Docodontan bauplan. This means that in spite of Castorocauda's specializations, it is still more primitive than any crown group mammal; even the earliest ones. The fact that Castorocauda represents an alternate branch, thereby demonstrating that there is no temporal discordance, renders lifepsyop's argument false and misguided.

"Docodonta lineages" and "mammalian synapomorphies" are no more than abstract objects used for classification. Also, you are merely asserting Castorcauda "represents an alternate branch", because in the evolution model, it would be expected to. All of your language here is fully loaded with and dependent on the metaphysical belief that Common Descent is true. Yet you seem to espouse these things as if believing you are stating empirical facts.

Additionally, as evolution is a non-linear process that does not necessarily occur at equal rates across time in groups or populations, the contemporaneity of derived and basal forms is entirely expected and well-documented both in the fossil record and in the present.

You are only clarifying the unfalsifiable nature of the evolution model. There is no robust way to gauge or test for temporal discordance in the fossil record, because it is "expected" that natural selection can make complex body plans appear hundreds of millions of years earlier than previously thought due to convergent evolution "experiments". It's just like "expecting" massive contradiction in phylogeny due to incomplete lineage sorting. Evolutionists believe by adding the "expected" disclaimer, they've avoided the ramifications of supporting an unfalsifiable theory.

It is not clear why the third sentence about fur was highlighted. For future reference, it's old news that fur is symplesiomorphic for mammals, and as such is never used as a trait in determining mammalian relationships.

It was only to show the increased silliness of having the first unambiguous appearance of fur in the fossil record be found on an aquatic mammal with a suite of traits previously considered to only belong to the body plans of 'advanced' mammals that didn't show up for another hundred million years. How malleable and jello-like the evolutionary model is, yet its proponents will continue to bluff that some elegant evolutionary morphological order is depicted in the fossil record.

 

[lifepsyop]

I've already presented very simple and rational reasons to expect such patterns in systematics. Similar phenotypes are built on similar genetics.

Tell that to wolves/thylacines and whales/hippos.

Are marsupial and placental reproductive systems similar phenotypes in your understanding?

 

[lifepsyop]

An Evolution journal? Dude, the ignorance is strong in you! The hell are you talking about? Even if Nature or Science was, like you call, an Evolution journal; why would it be impossible to submit a paper questioning anything. Do you have any idea how science works?

Why do you act so surprised? It is no secret that secular journals are aligned with Evolution worldviews.

The American Association for the Advancement of Science, and the publisher of the journal "Science" released this official statement: http://www.aaas.org/news/releases/2002/1106id2.shtml

"The contemporary theory of biological evolution is one of the most robust products of scientific inquiry. It is the foundation for research in many areas of biology as well as an essential element of science education. "

This is a creed. We're promoting Evolution, period. End of discussion.

It is quite simply, and admittedly, an 'Evolution' Journal. What's so hard to admit about that?

Evolution is a multi-national industry with a great deal of vested interest and stakeholders. What you are essentially suggesting is that an industry publish viewpoints that encourage itself to be dismantled. It makes no sense.

How the fuck would we ever progress in science if we were not able to question anything and everything?

You can question whatever you want scientifically. Just don't challenge metaphysical belief systems that your department heads believe in and have invested their careers into.

I myself am at the verge of publishing a paper questioning a 10 year old paper that has been cited over 100 times (I am a marine biologist btw). Just because you're paper goes against a certain paradigm doesn't mean you can't publish it.

It's the difference between challenging business practices within a company, and suggesting the company should open discussion for terminating itself. Try the latter and you will be shown the door.