Unfalsifiable Phylogeny

[he_who_is_nobody]

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

No, they are not. Nevertheless, you have missed the point of my statement completely. You claimed, “Similar phenotypes are built on similar genetics.” However, with my examples I demonstrated two animals with similar phenotypes, but vastly different genotypes and two animals with vastly different phenotypes, yet similar genotypes, which renders your statement false.

:lol:

It appears you do not grasp the reason behind the photo. Again, you claimed, “If the fossil record is anything, it is a dominant pattern of major types of lifeforms existing as distant islands of morphospace, largely lacking in intermediate connections” and “…there is no ‘matching temporal’ order of the fossil record.” Yet, that photo alone renders both of your claims false. Furthermore, it also appears that you have tacitly admitted that chimpanzees and humans are closely related, seeing as how you used a photo of dog skulls compared to a wolf’s skull when trying to make a point about skull diversity.

I am also going to start quoting my challenges to you in every post. You seem to be missing them and I do not know why.

I am not affirming the consequence; I am basing a conclusion on the evidence. We have fossil, genetic, and observed laboratory evidence to base these conclusions on. We also know that allelic changes in a population are the only thing that causes these changes. No one is affirming the consequences; there is evidence that points to this as the conclusion.

Furthermore, it appears you are claiming that kind is equal to family/genera, thus all I have to do is show an example of a change above family/genera to show that allelic frequency change can and does lead to population change. Is this a correct statement to make about your position?

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.

 

[DutchLiam84]

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.

I wonder why I am surprised...you're a conspiracy theorist (and a moron but that's just my opinion).

I have no idea what else to tell you. You live in a bubble mate.

 

[lifepsyop]

It appears you do not grasp the reason behind the photo. Again, you claimed, “If the fossil record is anything, it is a dominant pattern of major types of lifeforms existing as distant islands of morphospace, largely lacking in intermediate connections” and “…there is no ‘matching temporal’ order of the fossil record.” Yet, that photo alone renders both of your claims false. Furthermore, it also appears that you have tacitly admitted that chimpanzees and humans are closely related, seeing as how you used a photo of dog skulls compared to a wolf’s skull when trying to make a point about skull diversity.

I am also going to start quoting my challenges to you in every post. You seem to be missing them and I do not know why.

Apparently the dog image went right over your head. It simply shows how a single "species" can have extremely varied morphology, absent of any mystical evolutionary progression.

This means any collection of fossils you believe show an evolutionary progression of pre-human hominids to modern humans can simply be representing the same modern human species in segregated gene pools or under varied epigenetic effects of phenotypic plasticity.

As usual with evolutionary religious claims, the "hominid evolution" skull transitions rest purely on assumptions and speculation.

 

[lifepsyop]

I wonder why I am surprised...you're a conspiracy theorist (and a moron but that's just my opinion).

I have no idea what else to tell you. You live in a bubble mate.

Wow, what a thoughtful response. I had no idea that suggesting businesses will defend their self-interests was such a fringe concept. :roll:

 

[he_who_is_nobody]

Apparently the dog image went right over your head. It simply shows how a single "species" can have extremely varied morphology, absent of any mystical evolutionary progression.

This means any collection of fossils you believe show an evolutionary progression of pre-human hominids to modern humans can simply be representing the same modern human species in segregated gene pools or under varied epigenetic effects of phenotypic plasticity.

As usual with evolutionary religious claims, the "hominid evolution" skull transitions rest purely on assumptions and speculation.

Nope I did not miss that point; I even pointed that out in the section you quoted. However, what you seemed to miss is that the image I provided has a picture of a chimpanzee skull and a human skull. The rest of those are hominin skulls that perfectly link the two in both morphology and chronology. Those are observations, not assumptions or speculations. Additionally, whether the skulls belong to one or more species of hominin is an interesting discussion to have, but that discussion is far outside of your league. Furthermore, you seem to be claiming that all the skulls are modern human species in segregated gene pools (forgetting that segregating gene pools is a key in evolution). Are you trying to claim that modern humans can have skulls almost identical to chimpanzees?

I am not affirming the consequence; I am basing a conclusion on the evidence. We have fossil, genetic, and observed laboratory evidence to base these conclusions on. We also know that allelic changes in a population are the only thing that causes these changes. No one is affirming the consequences; there is evidence that points to this as the conclusion.

Furthermore, it appears you are claiming that kind is equal to family/genera, thus all I have to do is show an example of a change above family/genera to show that allelic frequency change can and does lead to population change. Is this a correct statement to make about your position?

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.

 

[DutchLiam84]

I wonder why I am surprised...you're a conspiracy theorist (and a moron but that's just my opinion).

I have no idea what else to tell you. You live in a bubble mate.

Wow, what a thoughtful response. I had no idea that suggesting businesses will defend their self-interests was such a fringe concept. :roll:

Your lack in understanding science cropped in one sentence.

I ask you again, how the fuck would we have ever progressed in science if what you say is true? Scientific advancement is absolutely impossible if they pick and choose papers the way you say. We would still be teaching phrenology, alchemy and astrology as if they were correct science.

My paper would never be accepted either because I found a (possible) flaw in a 10 year old paper by some very famous scientists (in my field). These scientists happen to be editors for the very same journal I'd like to publish it in.

If I had valid evidence against the theory of evolution you be damn right I sent it to Science or Nature. I'd become very famous. How many times do we have to tell you this? Why don't you understand this?

Are you a scientist or studying to become one? If so, take a class in science philosophy, it would help you a lot.

 

[scalyblue]

#be op
#get a swimming pool full of steel ball bearings.
#drop them from a helicopter onto a perfectly level parking lot.
#ball bearing chaos, cars ruined, kittens killed, families destroyed
#Watch them clatter and roll until eventually every single one of them lines up into writing
#Witnesses them spell out "Check for magnets under the asphalt you fucking idiot!" in twenty seven different languages including binary and Esperanto.
#gather them up again and repeat a dozen times with the same results
#so much blunt force trauma
#find a stray, gore covered outlier trying to roll into formation
#pick it up and jump up and down in excitement
#shout "That magnet theory is a bullshit conspiracy!"

 

[Master_Ghost_Knight]

Apparently the dog image went right over your head. It simply shows how a single "species" can have extremely varied morphology, absent of any mystical evolutionary progression.

Did I heard that right. Are we being punked? How exactly do you explain the variety of morphology in dogs?
The fact that they are still the same species is incidental. It's a slam dunk. Are you not able to compute the consequences of your own arguments? How can you not immediately realize that you just defeated yourself the moment you made that statement? How could this be more obvious?

 

[Isotelus]

The second portion of the quote is from an earlier response addressed to Rumraket. My response also addresses the last quote so I have included it here.

"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.

They are similar kinds of animals. People have known that for thousands of years. It's not surprising that they group together. Have you advanced anything but metaphysical assumptions that such groupings should not exist absent of Common Descent?

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.

It is not a consistent or cogent argument to reject the means by which animals are classified while agreeing similar animals naturally group together, and therefore not a robust refutation of common descent. Whether or not common descent is true, if you agree that those shared similarities are what unite the group, then they are directly observable and above assertion, and as such should not be dismissed as merely abstract means of classification. Likewise, if you accept Castorocauda as a mammal, then you also cannot simultaneously dismiss the parameters by which it is allied to mammals and those which may remove it. Moreover, if you understood the proper definition and application of a synapomorphy, you would not be implying that the aquatic adaptations in question are themselves advanced and useful traits that can define or classify a group, or that the presence of them in an animal whose entire skeletal morphology is unlike any modern taxa is unreasonable grounds to call it non-ancestral. It would also be extremely tenuous and rather stupid to assume that C.lutrasimilus does represent a common ancestor of modern taxa, both for the reasons above and because there is no justification to assert any fossil found will be a direct ancestor to any living representative.

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.

My statements are made with consideration and research and I state nothing that I cannot substantiate. I also dislike having to repeat myself. I did not say temporal discordance is expected; I said it does not exist. Expectations are based on repeated observations, and my comment that it is normal for derived and basal forms to be contemporaneous is explainable in the fossil record because it is both observable and demonstrable in modern faunas. For the sake of argument, I can agree that there is a gap, but absence of evidence is not necessarily evidence of absence. As terrestrial insectivorous, terrestrial carnivorous, scansorial, and fossorial mammal forms (note that Castorocauda also has fossorial adaptations) persist throughout the Mesozoic and into the Cenozoic, the assertion that the gap in semi-aquatic and volant forms is evidence of temporal disorder and against common descent is unjustified. The lack of such forms resulting from poor sampling is a distinct possibility that deserves consideration. Scalyblue’s above quote applies to this directly. From another angle, you used the Wikipedia quote concerning Eocene semi-aquatic adaptations without realizing it is referring to placental mammals only. Recalling that C. lutrasimilus was also compared to the platypus, it should be noted that semi-aquatic forms of early Monotremes have been found in the early Cretaceous, and thus far the earliest Ornithorhynchids come from the early Paleocene. The hundreds of millions of years gap between aquatic adaptations is non-existent regardless of whether Castorocauda is a crown mammal or not. Hwin also made an additional point that I’ll reiterate: The “expectation” of Mesozoic mammals to be predominantly small, generalized and shrew-like is not even directly addressing any aspect of natural selection or evolution in general, but a remark on the trends observed in the fossil record itself prior to the discovery of an ecomorphologically diverse set of mammal relatives.

 

[Dragan Glas]

Greetings,

It seems to me that everyone is getting bogged down in details in this debate.

Basically, the argument can be summed up in this way:

Evolution can be thought of as a flow of water - The River Of Life - hailing from its origin in the mountains of its distant past: abiogenesis.

You're standing on the bank of The River watching it flow past you *that way*.

lifepsyop comes along and points out eddies, micro-currents and cross-currents in The River and claims that these prove that The River isn't flowing *that way* - yet won't (or can't) say which way it's flowing.

So, who's right?

Scientists (here and elsewhere), Rumraket (citing scientific papers), Isotelus, HWIN, MGK, Inferno, Dustnite, Darkprophet232, DutchLiam84, herebedragons, Engelbert, Dave B., Idmitruk, scalyblue, me et al who all claim that The River flows *that way* or lifepsyop who claims it doesn't flow *that way* and anyone who claims that it does is part of a vast conspiracy.

Kindest regards,

James

 

[he_who_is_nobody]

Apparently the dog image went right over your head. It simply shows how a single "species" can have extremely varied morphology, absent of any mystical evolutionary progression.

Did I heard that right. Are we being punked? How exactly do you explain the variety of morphology in dogs?
The fact that they are still the same species is incidental. It's a slam dunk. Are you not able to compute the consequences of your own arguments? How can you not immediately realize that you just defeated yourself the moment you made that statement? How could this be more obvious?

The doublethink is strong in this one.

 

[Rumraket]

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.

Yes, because they were inherited from a common ancestor, not because of design constraints. Why can't you fathom this? This constraint is entirely imagined. There'd be no actual physiological reason to do it. You could in principle erect almost any concievable underlying genetic framework for some arbitrary phenotype.

This is where you ad-hoc that your designer re-used older designs, but I've already dealt with this.
You argue that you designer takes something it's already designed, then uses this former design as a template for a new similar one. But that rationalization here doesn't actually explain the observed pattern. Particularly thousands of dead and broken pseudogenes and ERV insertions, drifting randomly under the accumulation of neutral mutations. Create them in the first place?

Not to mention the fact that your entirely imagined designer is supposedly also changing his pseudogene insertions every time by inserting mutations into them. For zero fucking reason.

And then there's the enhancer and promotor regions your designer also copy over every time, AND THEN MUTATE. WHY? Why the FUCK would the designer mutate them? There's no reason to do that if they worked fine in the previous organism. And we know that they do, we understand perfectly well how things like initiation of transcription, replication or inibition work at the atomic and molecular level.

You've given zero response to this point, it's been ignored completely. Your designer is postulated, according to YOU, to take his older designs, copy them over into newer creations. That's your argument for why we should expect to find nested hiearchical arrangements of the genomic and morphological features of organisms.

But if that's the case, why doesn't your designer ACTUALLY do that? It seems they change ever so slightly every time they're "copied" into a new organism. And that change is mostly neutral or silent, meaning there's be no REASON for that change to exist.

IT GETS EVEN WORSE:
The TYPES of neutral and silent mutations we find in the "copies" of "older designs" are EXPECTED FOR BIOCHEMICAL AND PHYSIOLOGICAL REASONS. Your designer is therefore, according to your rationalization, designing in a bias towards transversions over transitions, a bias towards gene-duplications in regions already emprically established to be prone to unequal crossing over(which is the most primary CAUSE of gene-duplications).

Why, WHY would you designer prefer to design in NEUTRAL TRANSVERSIONS over NEUTRAL TRANSITIONS, when this is already expected for known biochemical reasons?

WHY would you designer prefer to deliberatel design in gene-duplications IN REGIONS OF THE GENOME NATURE ITSELF IS MOST PRONE TO MAKING DUPLICATIONS IN? Isn't that just a TAD BIT too coincidental?

The unescapable conclusion is therefore that your designer is seemingly doing everything in it's power to make it look like these genetic changes arrived through natural biochemical mutational mechanisms, not by design.

Here your re-use of older designs retort becomes laughabl ad-hoc. Your only course here is simply to assert that "the designe wanted it that way".
Which means, yes, the designer wanted it to look like they simply mutated slowly over time.

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.

I've said a tad more than that I'm afraid. Everything I just said above, I already said in my previous posts, but you've elected to ignore it and produce a simplistic caricature of my full argument instead. I wonder why. Actually, I do not.

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.

This is coming from the guy who QUOTED THE FUCKING BIBLE in this thread. Are you the biggest, most hypocritical joke of all time?

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".

No, because the designer YOU POSTULATE AS BEING RESPONSIBLE is ALSO known to be considered PRACTICALLY UNCONSTRAINED IN CAPABILITY.

You simply can't get around your own contradictory argument here. You reason from constrained human design paradigms to the conclusion that the designer is an omnipotent supernatural god. These are all YOUR postulates. You will excuse me if I don't give a shit that you whine when I use your own faulty, ambivalent reasoning against you.

Either you know something about you designer and what it would be expected to do when it does designs, so that we can scientifically test those postulates though observation, or you do not, in which case you should shut up and accept a probabilistic evaluation.

And actually it IS "more probable", not just "possible". You keep getting that wrong too.

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.

You could, and this claim could then be empirically tested by measuring the approximate rate of de-novo gene origination in evolving laboratory populations of organisms. If your hypothesis did not match observation, then in the words of famous physicist Richard Feynman, "it's wrong".

Tell me, does your postulate here match observed de-novo gene origination rates in evolving laboratory populations? No you say.

Then allow me to quote Feynman again: "IT'S WRONG".

This explanation is already used.

[Citation needed]

There is no barrier to this process happening in greater degrees and frequencies within your model. </B>

Except I alread told you what that barrier would be: Expected (for empirical and statistical reasons) mutation rates and generation times.

There's more to this argument, such as the expected statistical frequency with which established junk-regions could be postulated to acquire gain-of function and initiation-of-transcription mutations and just so happen to produce functional protein-coding genes.

You keep forgetting the statistics. Probably because you're absolutely clueless about the methods. Actually, I know you are, as I shall demonstrate beyond all shadow of doubt when I proceed to deal with that intergalactic void of comprehension you've produced in you response to my citations on ancestral sequence reconstruction.

<B>Evolution would "explain" the absence of the pattern you are ranting about being overwhelming statistical evidence for Common Descent.

Except that I have now explained why it would not, so you've simply MADE SHIT UP.

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.

Oh look, it's the gaps-in-the-fossil-record-argument just reworded. Does it even get any more creationist than this?
This picture shows the moment when the builders of the bridge over Sydney harbour gave up their project because it had become obvious the ends would never join up:

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 yet we have those transitional forms. Mysteriously placed chronologically approximately where expected in geological strata. Weird, right?

And there is no "matching temporal order" of the fossil record.

Is that right?
Then you'll have no problem explaining how just this simple exposition on pre-cambrian and the cambrian fossil record is wrong:

1. Before 700 mya, maybe well before: Single-celled eukaryotes (acritarchs)
2. Earlier Ediacaran: Multicellular animal eukaryotes, but simple, sponge-grade organisms
3. Later Ediacaran: Multicellular animal eukaryotes with more complexity, i.e. cnidarian-grade organisms
4. Very late Ediacaran: Simple slug-grade/worm-grade organisms (at least their tracks and burrows) – the first ones only making surface tracks and lacking burrowing ability. Making tracks suggests that the organisms have at least a front end and a back end, a mouth, anus, and gut connecting them. These are almost certainly bilaterians.
5. Very late Ediacaran: The very first biomineralized “skeletons”, e.g. Cloudina, basically a worm secreting a tube, as well as the first evidence of predatory boring. Cloudina gets no mention at all in Meyer’s book.
6. At the beginning of the Cambrian, we start to see more complex burrowing – e.g., vertical burrowing through sediment, clearly indicating worm-grade organization and an internal fluid skeleton, i.e. a coelom. The burrows gradually increase in complexity over 10 my.
7. Small shelly fauna: The shells, which started very small and very simple, gradually diversify and get more complex, radiating especially in the Tommotian. By the end of the Tommotion, some of the “small shellies” can be identified as parts of larger, “classic” Cambrian animals. The Tommotian is an utterly key period for any serious discussion of the Cambrian Explosion. Unfortunately, the word “Tommotian”, or any equivalent terminology (the detailed stratigraphy of the Cambrian is still being worked out, see Erwin & Valentine 2013 for a review), does not even appear in the book! The Small Shelly Fauna (SSF) gets just one (one!) mention in the book, buried in endnote 27 of Chapter 4, a whole chapter devoted to debunking the idea that the Ediacaran fauna is “ancestral” to bilaterians. (See discussion of the concept of “ancestral” below, which Meyer makes a complete hash of; however, I would tend to agree that the evidence is not good that the classic Ediacarans are within the bilaterian crown, as much because of the late date of #4-6, above, as anything.)
8. The earliest identifiable representatives of Cambrian “phyla” don’t occur until millions of years after the small shelly fauna have been diversifying, and they tend to be taxa on the stem below the crown of living phyla, rather than placeable within the crown. Trilobites are an exception, but what is often missed is that deposits like the Chenjiang have dozens and dozens of trilobite-like and arthropod-like organisms that fall cladistically outside of these respective clades. These are transitional forms! How can this fact not be highlighted!?!
9. In general, the earliest Cambrian relatives of the living phyla tend to be a lot more wormlike or sluglike than most modern representatives of the living phyla. Of course, many of the living phyla are basically still worms, and the more complex living phyla (e.g. molluscs, chordates) have early-diverging representatives or relatives that are rather more wormlike than the better-known representatives with more complex bodyplans. Even the earliest “fish” – actually either stem-group craniates, stem-group cephalochordates, or stem-group chordates – are basically filter-feeding worms that happen to swim. They don’t have jaws, scales, limbs, a bone skeleton, or anything else that most readers would associate with the word “fish”.

We could go on through the fossil recod after the cambrian period too, and talk about why it is lobe-finned fish unambigiously predate all fossils on the fish-tetrapod transitions.
For example, why is the oldest known sarcopterygian (lobe-finned fish) fossil 418 million years old, with that general trend continuing until about 385 Myr in Eusthenopteron. 5 million years after which we find things significantly more amphibian-like, ala Panderichthys from 380 Myr and on. Then at about 375 Myr we find the now-famous Tiktaalik fossil.

On the subject of Tiktaalik, if the fossil record is just some jumbled together just-so story of paleontology, how come the species was predicted to exist in fossil strata of approximately 375 Myr before it was even known to exist?

Moving on, how come Ichthyostega, which is even more tetrapod-like than Tiktaalik, is only found in younger strata than Tiktaalik and the rest, at approximately 374 Myr and on?

How com Acanthostega and similar organisms, which is more or less a complete tetrapod, is only found in strata 365 Myr and younger?

How come Hynerpeton is only found in strata 360 Myr and younger?

Why do we find similar such chronologically supported transitions from dinosaurs to birds(the first dinosaurs unambigously predate the first birds, or even the first bird-like dinosaurs), or from terrestrial mammals to whales?

Why do dinosaurs in general emerge way before birds and mammals anyway? I'm by no stretch a biologist or paleontologist, so my knowledge of comparative anatomy and the fossil record is pretty rudimentary and basic at best, but even here with the few things I've mentioned your ridiculous claims have had a 3000-ton freight-train run through them at 200 mph. There is nothing left but smoking debris.

From a distance, there is only a vague sequence of the major types of life.

As elucidated this claim of yours is demonstrable horseshit.

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.

Bla bla bla.... :roll:

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.

Higher mamals? Adaptations for air and water? What the fuck are you even talking about? I'd like to see actual references here that all these claims you're making are actually expected by professional taxonomists and paleontologists.

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.

Wow, thank you, I didn't know that mammals weren't allowed to coexist with other contemporaries. You know that speciation happens by population splitting, right? That means there's now two independet pupulations where before there was only one. In other words, we expect multiple populations simultaneously coexisting, showing a variation of the degree of adaptations to a range of niches. That's why even though tetrapods did eventually evolve, fish continued to exist.

How is this a suprise to you? Did they forget to talk about mechanisms of speciation or evolution as a population-level phenomenon in creationist homeschooling? Or that multiple independent niches coexist, both geographically isolated and not. Meaning if a population splits with the one of the two branches adapting to a new niche, you expect to have the "transitional species" coexisting, if not geographically then at least contemporaneously with a population more similar to it's ancestors.

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:

Why is that comical? Whales have converged on the same basic bodymorphology as fish, despite having evolved at least 300 million years later. Could it be that there are certain physical constraints in common, shaping the evolution of many distinct lineages? What could that be? Oh, reduction of hydrodynamic drag?

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!

Now the dating is wrong too? Did you get a degree in geochronology while I was away? Shouldn't you first actually attempt to comprehend the subject you set out to criticize to begin with?

But the point is, again, how flimsy the case is for Common Descent, and how well-insulated it is from falsifiability.

There are precambrian rabbits?

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.

No, what we find is your personal complete lack of understanding of evolution as a branching pattern, population-level phenomenon under countless similar physiological constraints (natural selective pressures being highly similar all over the globe).

You just can't let go of your creationist ladder-thinking, with the strawman picture of evolution as a single great lineage going through stages

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

:roll: Vague and ambiguous equivocation.

Vague in what sense, equivocation between what?

It's simply a demonstrable fact. Do you have siblings? Do you want to take a bet on wheher you personally contain alleles that your siblings do not? That's incomplete lineage sorting right there.

You will also contain mutations that neither your parents or your siblings do. And your siblings will contain mutations that neither you nor your parents do. So will it be with your children, and hose of your siblings. And so on and so forth. Tell me, what pattern would we expect to find in the genomes of your all your decendants a million generations from now?

Oops! "Vague" in no way at all. And the accusation of equivocation is empty in all concievable ways.

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.

Fact.

A pattern results from comparative studies on biology.

Yes, a pattern results. But what pattern? There is no expectation for a particular one without some kind of underlying mechanistic framework producing specific subsets of all possible patterns. The one pattern we do observe is only corresponds to a small fraction of the total set of all possible patterns, the pattern that coresponds to a branching, population level phenomenon of descent with modification. This is what we obseverve.

Such a pattern can be rationalized on a "design" hypothesis, but ANY pattern can. That means the evidence is a significantly stronger indicator of evolution, than design, simply because evolution only produces similar such patterns, while design can produce an infinity of different patterns.

You can add further elaborations to your design hypothesis to increase the probability of the evidence, in which case you just end up with a significantly more improbable prior probability of your hypothesis.

That's basic bayesian logic, the consequence of which is that design is exceedingly improbable. And remember, we've still not seen your mysterious designer, while evolution, including all the mechanisms. is and will always remain an observed fact.

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.

No it cannot. It would be massively statistically unlikely for the same underlying genetic framework to evolve in the same way twice if the two species in question did not inherit their starting points through close common descent and was not subject to the same or highly similar selective constraint.

You know that convergence is sometimes proven false statistically, right?
Here's an example:
An empirical test of convergent evolution in rhodopsins
Kristine A. Mackin, Richard A. Roy and Douglas L. Theobald
http://mbe.oxfordjournals.org/content/early/2013/09/27/molbev.mst171.abstract

Abstract

Rhodopsins are photochemically reactive membrane proteins that covalently bind retinal chromophores. Type I rhodopsins are found in both prokaryotes and eukaryotic microbes, while type II rhodopsins function as photoactivated G-protein coupled receptors (GPCRs) in animal vision. Both rhodopsin families share the seven transmembrane a-helix GPCR fold and a Schiff base linkage from a conserved lysine to retinal in helix G. Nevertheless, rhodopsins are widely cited as a striking example of evolutionary convergence, largely because the two families lack detectable sequence similarity and differ in many structural and mechanistic details. Convergence entails that the shared rhodopsin fold is so especially suited to photosensitive function that proteins from separate origins were selected for this architecture twice. Here we show, however, that the rhodopsin fold is not required for photosensitive activity. We engineered functional bacteriorhodopsin variants with novel folds, including radical non-circular permutations of the a-helices, circular permutations of an eight-helix construct, and retinal linkages relocated to other helices. These results contradict a key prediction of convergence and thereby provide an experimental attack on one of the most intractable problems in molecular evolution: how to establish structural homology for proteins devoid of discernible sequence similarity.

Funnily, Theobald is again in the spotlight in this thread. Doing the very thing you're claiming evolutionists would never do, actually test claims of common descent and convergence. Using the very same methods you've repeatedly ignored. How does this fit into your grand metaphysical research-paradigm conspiracy theory?

Any pattern of shared phenotypic traits can be "explained" by both common descent and convergent evolution.

No, it can't. Again you're missing the point about degrees. About statistics.

If we consistently found higly similar complex traits in multiple species with very remote ancestry, this would beg an explanation outside the current evolutionary paradigm, because it simply wouldn't be able to explain such freak occurrences over and over again. There would have to be something else going on than mere convergence due to similar selective pressures.

The thing about convergent phenotypical traits is that they're usually not very complex. Or when they're similar, they're usually only superficially similar. The more complex and similar the trait, the more closely related the species, otherwise the recurrence of highly similar convergent traits starts to become an untenable postulate under evolution. It would simply be too unlikely.

When we see both highly complex and similar convergent features, descent is always close. When we see less complex but still similar convergent features, descent is further back.

Take whales and bats with their echolocation. Descent is relatively close, they're both mammals, having inherited their hearing apperatus and the majority of the genome from a mammalian common ancestor. Their echolocation apperatus is both similar and complex, due to both close descent and similar selection pressures.

Going much further out between whales and fish, convergent evolution has created similar bodyshapes for the reduction of hydrodynamic drag. This is a much less complex convergent trait, again makes sense on evolution. Now if fish had been found with echolocation and the physiologies and distributions of organs and genetics had been as similar as between bats and whales, we'd have a problem. But that's not what we find.

Any pattern of genetic sequences with no signal of common descent (Orphans) can be "explained" by "de novo" evolution.

Again statistics would make a mockery of that kind of blind ad-hoc declarations. First of all, large quantities of ORFan genes would have to fit genome evolution rates of the species in question, which means they'd be most frequent in fast evolving lineages with short generation times that cover many large areas and niches. We see this perfectly exemplified in insects, many kinds of fungi, single-celled eukaryotes and of course bacteria and archaea, which are pretty much ubiquitous in all environments on the planet.

If large quantities of ORFan genes were found in, for example humans, with zero DNA sequence homology even in junk regions of closely related species such as chimps, we'd have a problem.

But this gets us to an important point about ORFan genes, what they are and how the claim of de novo ORFan gene evolution can be tested. Instead of looking for orthologous protein-coding sequences in sister taxa (which you'd normally do), you simly look in the junk regions of a sister taxon.

Why? - Most ORFan genes are generated by resurrection of junk regions through reactivation of long-dead promotor and enhancer regions, or through new start codons and many similar phenomena. That means if a species is found to have a large portion of ORFan genes, we should be able to find homologous sequences in the junk regions of the genome of closely related taxons. Heck, even sometimes, because of large frequency of transositional activity in the junk regions, we can even find homologous DNA sequences in the junk regions of the very same taxon found to have many ORFan genes, because after many subsequent transposon insertions, eventually a mutation in one of these regions resurrects an old promoter region or start codon, leading to a new protein product.

So again, even ORFan gene generation can be tested. Where do they happen? How much? Homologues in junk regions?
All these questions must fit certain constraints within certain limits.

Any pattern of phylogenetic discordance can be "explained" by incomplete lineage sorting.

Already been over this. Statistics, statistics and more statistics.

Of course, there's also the fact that incomplete lineage sorting is literally unavoidable with the extant mechanism of inheritance. You will have a different sortiment of genes than your siblings, unless you're monozygotic twins. This will just always be true.

Fuck, even if evolution is false and biblical "kinds" are somehow the true magical constraint on speciation, given what we know of genetics and inheritance, incomplete lineage sorting would STILL be expected. Simply, the total sortiment of genes from both parents aren't passed on to any single offspring. The mere observation that Incomplete lineage sorting has taken place can falsify neither evolution nor design.

To construct an argument against evolution here, you would have to have extremely high amounts of it occurring so often it would be absurd to think it just happened through chance alone.

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.

Of course you are, that's all you're doing. You're postulating magical instantaneous creation through recurent usage of "similar designs". That's been your go-to alternative explanation of the pattern every time. I've simply explained how this rationalization still doesn't actually explain the observed pattern.

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.

Clearly, I have proven the exact opposite is the case. The problem has been that you don't actually understand any of the methods required for falsification.

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.

The funny thing is that doesn't actually logically follow. Even if god did actually magically create life, it still wouldn't follow logically that life could not also emerge naturally. You'd have to posit an additinal assumption, that god purposefully arranged for the cosmos to disallow the gradual emergence of life through natural physical and chemical means. But how could you even know that? It doesn't say that god did anywhere in the bible, so you'd have to simply believe it on blind faith.

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).

Nobody believes in spontaenous generation. The simplest models of abiogenesis still invovle pretty long periods of chemical evolution powered by natural physical cycles before we get to anything that even remotely resembles something like a cell. But that's another matter entirely. We don't know how life originated so that's all we can say at the moment.

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.

Falsification of the bible through proving biblical "kinds" true, that's just funny mate. So you really do think evolution would poduce crocoducks?

I will be back later with a veritable lecture on ancestral sequence reconstruction.

 

[Rumraket]

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"

As we shall see, this claim of yours will be put to a direct qualitative test by none other than Discovery institute bioengineers Douglax Axe and Ann Gauger, who in their ironic attempt to disprove evolution, end up disproving design and confirming evolution. But before this simultaneously most hilarious and sad exposition, let's look at ancestral sequence reconstruction itself and your inane objections:

, 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.

You have completely misunderstood what the above list shows. Contrary to your assertion, the above sequences were not extracted from inactivated regions of extant life, they were COMPUTATIONALLY DERIVED BY AN EVOLUTIONARY ALGORITHM using statistics that ASSUMES our current knowledge of how molecular evolution takes place.

In other words, they take a collection of sequences in extant life, assumed to be homologous, then they calculate the most probable ancestral sequence using our understanding of evolution. the algorithm then produces a most probable consensus sequence.

Taking this sequence, which is then referred to as an "ancestral homologue" (which is that list you see above, a list of mathematically inferred ancestral versions, derived using statistics from sequences in extant life), they build the corresponding gene sequence using modern biotechnology. They then take this gene, insert it into a plasmid, transfect into a bacteria who faithfully expresses the requisite protein product.

They then extract this protein product from the bacteria and test it's properties experimentally.

In this respect, ancestral sequence reconstruction constitutes a DIRECT QUALITATIVE TEST of evolutionary postulates about the history of life and molecular evolution.

Quite simply, if evolution was false, there would be NO REASON TO EXPECT SUCH STATISTICALLY INFERRED SEQUENCES TO CODE FOR FUNCTIONAL PROTEIN PRODUCTS AT ALL.

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.

No, it is manifestly NOTHING like that. You don't seem to fathom how this kind of gene sequence reconstruction actually works.

There is nothing about "location" involved at all. It has everything to do with looking at the actual sequences, constructing the best fitting phylogenetic trees, then taking your tree and inferring an ancestral node. That means a consensus sequence from which all the extant orthologous sequences most probably derived.

These sequences are not changed directly from one into the other and then from that into a third, as your design hypothesis would seem to imply. Instead, when you have three homologous sequences, they all derive from a different common ancestor.

That common ancestral sequence is not just some haphazard chimeric sequences somewhere halfway between the three(and it isn't that sequence 3 was derived from sequence 2, which was derived from 1), it is an independent, unique sequence that got isolated in two independent lineages, and then subsequently suffered independent mutation in each of those, of which one again underwent a "speciation" event.

Since we know something about molecular evolution, such as the types of mutations that happen most frequently, we can employ this knowledge in trying to reconstruct these "assumed" ancestral versions of the genes.

When we do that, when we use those algorithms and reconstruct these ancestral nodes, we are testing the evolutionary postulate that they derive from a common ancestor that was different from all three (or more, depending on how many orthologues are used to reconstruct the history). Exactly because if common descent was false and the inferred evolutionary history never took place, there would be no expectation that this inferred ancestral sequence would be find to be functional.

If there is one thing that half a century of molecular biology has shown us, it's that you can't just haphazardly mutated extant protein products from one directly into the other and still expect to get a functional enzyme or structural element. While there may be many functional polymers in sequence space, there aren't THAT many.

Here we have a small list of none other than ID proponents and Creationists affirming exactly this claim:

CREATIONISTS and Intelligent Design proponents themselves have stated clearly that every and all mutations are CATASTROPHIC. Remember that? "Catastrophic."

Every human baby born has somewhere between 100 to 200 more mutations than its parents (depending on how you count)-- and twice that number relative to its grandparents-- and thrice that relative to its great-grandparents-- etc.

Young Earth Creationist Kent Hovind: “A change of only three [DNA] nucleotides is fatal to an animal. There is no possibility of [genetic] change.” (Ken Hovind, Source: http://media.drdino.com/sem/audio/mp3/books2.mp3 @ 82:10, March 2003, cited at http://kent-hovind.com/quotes/sciencei.htm)

Got that? Kent Hovind says only three mutations will kill an animal.

If creationism is correct, every baby has 100 to 200 new CATASTROPHES its parents didn't have-- and twice that number of CATASTROPHES relative to its grandparents-- and thrice that relative to its great-grandparents-- etc. Enough to kill every baby on Earth a hundred times over.

Pro-ID Philosopher William Dembski: “[T]here is now mounting evidence of biological systems for which any slight modification does not merely destroy the system’s existing function but also destroys the possibility of any function of the system whatsoever.” [Dembski, The Design Revolution, p. 113]

Pro-ID lawyer Phillip Johnson: “Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations…make birth defects” ["Berkeley's Radical: An Interview with Phillip E. Johnson", November 2000.]

Pro-ID lawyer Edward Sisson: “[T]he theory of unintelligent evolution, which depends entirely on the supposed occurrence in history of trillions of DNA mutations that beneficially affect body shape, has not identified any such mutations” -- [Edward Sisson, “Darwin or Lose”, Touchstone, v. 17, issue 6, July/Aug. 2004]

Uncommon Descent: “As far as I know, the current consensus of population geneticists is that mutations do indeed have disastrously bad fitness.” [Eric Holloway. Uncommon Descent. August 28, 2011.]

Young Earth Creationist Henry Morris: “Inheritable and novel changes (mutations) which take place in organisms today have always been observed to be harmful.” [Henry Morris, The Remarkable Birth of Planet Earth, p.vii]

Young Earth Creationist Duane Gish: “the mutations we see occurring spontaneously in nature or that can be induced in the laboratory always prove to be harmful.” [Gish, Evolution? The Fossils Say No, p. 47]

Duane Gish: “all mutations are bad” [Gish, Dinosaurs by Design (1992), p.83]

Duane Gish: “Remember, all the changes were just mistakes, they were genetic errors, mutations, almost everything which is bad… they're all bad” [Keith Saladin-Duan Gish Debate II, 1988]

Creationist Don Boys: “Not only are mutations always harmful, but they produce changes in present characters, never producing new characters. Mutations are the catalyst for defects, deformity, disease, and death; yet evolutionists scream that they are the explanation for all the varieties we see… [T]he results of all mutations: disorder, defects, disease, deformity, and death.” -- ["Almost a Thousand Major Scientists Dissent from Darwin!", Don Boys. Canada Free Press. May 2, 2010.]

Muslim Creationist Harun Yahya: “[N]ot one single useful mutation has ever been observed… The slightest alteration in [genetic] information only leads to harm.”

The Muslim creationist sex-cult of Harun Yahya says all mutations cause only harm: “Mutations… like all accidents, they cause harm and destruction. The changes effected by mutations can only be like those experienced by people at Hiroshima, Nagasaki, Chernobyl … freaks of nature… because all efficient(?) observable mutations cause only harm to living things.”

There we have it. All the creationist top dogs and professional ID proponents of the discovery institute go out of their ways to tell us that introducing mutations to extant functional DNA and proteins will invariably always lead to loss of function and dead sequences. Mutation just cannot create anything new that works. This is their claim.

It doesn't stop there, because we can go to a DIRECT EMPIRICAL TEST DONE BY DISCOVERY INSTITUTE PROFESSIONALLY EMPLOYED SCIENTISTS:
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1
The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
Ann K. Gauger, Douglas D. Axe

Abstract

Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs--the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations--transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl2), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF2). After identifying and testing 29 amino acid changes, we found three groups of active-site positions and one single position where Kbl2 side chains are incompatible with BioF2 function. Converting these side chains in Kbl2 makes the residues in the active-site cavity identical to those of BioF2, but nonetheless fails to produce detectable BioF2-like function in vivo. We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.

The great irony here is that Axe and Gauger directly test the design-postulate and ignore the evolutionary postulate.

They don't do ancestral sequence reconstruction and try to infer the most probable ancestral sequence using phylogenetic maximum likelyhood trees (as evolutionary biologists would have them do). Instead, they do what YOU'RE POSTULATING YOUR DESIGNER DID, they take one sequence (Kbl2) and try to directly convert it into another closely related homologue (BioF2), mutation by mutation.

They discover that doing this BREAKS THE FUCKING ENZYME. It stops working. Seemingly affirming the many claims of the creationists and ID proponents above.

But this is not what evolution postulates took place, this is NOT what is done with ancestral sequence reconstruction. Here both sequences (actually more, you need 3 orthologues sequences or more to do ancestral sequence reconstruction) evolved from a different common acestor to both of them, they did not change directly one into the other.

We would all like to thank Douglas Axe and Ann Gauger of the discovery institute propaganda laboratory to proving the design hypothesis false, and validating ancestral sequence reconstruction by showing that it would NOT be expected to find functional products by simply introducing mutations from one sequence into the other.

In conclusion, we have strong reason to believe that ancestral sequence reconstruction actually reconstructs ancestral genes, because, as just demonstrated, simply changing one sequence into another one mutation at a time will emphatically NOT produce a functional polymer.

I made a nice little drawing for you:

But when actual ancestral sequence reconstruction methods are used, functional sequences ARE found. As demonstrated aptly in all the papers I linked earlier. Therefore we have good reason to think the extant homologous proteins actually DID evolve FROM these resurrected by phylogenetic inference-sequences, and were NOT created through simple mutational change from one into the other.

What makes the results of these kinds of ancestor reconstructions even more robust is when they use resurrected nodes to further infer even more distantly related ancestral sequences. It would be absurd to postulate that you can keep inferring ancestors from already inferred ancestors and still get functional protein products if the reconstructed evolutionary relationship didn't actually take place.

It doesn't stop there either, because as was shown in the paper on the thermophilicity on ancient life, these kinds of ancestor reconstructions, going through multiple inferred to be ancestral nodes and further reconstructing even older ancestors, actually converge on a cluster of sequences that work best at a certain range of high temperatures. Let that sink in for a while (go back and read the goddamn papers). Multiple independent groups have tried to reconstruct the proteins from the last universal common ancestor (a hypothetical entity), focusing in each of their studies on a single protein. What the different groups found was that all their proteins worked best at temperatures around 70-90 degrees centigrade. That means an organism living in/near a hydrothermal vent of some sort.

But if these statistically inferred, different proteins did not ever exist in the same organism, why DO they converge functionally on a similar range of optimum temperatures?

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.

Literally clueless about ancestral sequence reconstruction. We're not talking about expression patterns being tied to morphological similarities for whatever physiological constraint you imagine we're talking about a direct qualitative test of the assumption of evolution from ancestral versions of extant genes.

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.

... are you serious? Am I truly reading this?

Are you seriously postulating that your unobserved designer actually first created the ancestral genes that no longer exist and THEN derived all extant variations from it?

Is it even possible to get any more ad-hoc? How can you even convince yourself that your designer operated like this?

Yes, yes, you can rationalize this too. You don't seem to fathom that ANY CONCIEVABLE OBSERVATION OR RESULT CAN BE RATIONALIZED BY DESIGN. The idea is literally unconstrained and you're directly proving it here.

Seriously, humor me. Tell me why we should find functional nodes in reconstructed phylogenies using methods that assume our extant knowledge of molecular evolution.

What IS your design-rationalization here? Do you really believe god made the nodes we find with ancestral sequence reconstruction and then derived the genomes of extant life from those nodes? So your god simply went OUT OF HIS WAY to make it look like life evolved?

 

[Rumraket]

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.

That isn't the claim. The claim is that enhancer and promoter regions (and their associated regulatory elements) are not physiologically constrained by the internal biochemistry of the organism to such an extend that they're required to be changed between different organisms.

To understand my argument here requires understanding what enhancer and promoter regions and their associated regulatory proteins are and how regulation works and what kind of constraints they are (and are not) under.

Long story short, certain genes are shut on and off all the time depending on local environmental circumstances of the cell. In order for a protein coding gene to be shut on or off, a regulatory element has to bind to a certain piece of DNA.

Now, let's say you just want to turn on a single gene that encodes an enzyme that you need to digest a carbohydrate you eat. For this to happen, a specific regulatory element needs to reckognize a specific sequence of DNA in your genome and ONLY that region. For this purpose, both the DNA region and the regulatory protein need to be specific enough, that means different enough from the rest of the genome, that only the specific gene is turned on/off when needed, and not something else which is unrelated or unneeded, which could end up being fatal if you're really unlucky.

In order to achieve this level of specificity that ensures that only that one gene is shut on/off, the specific DNA sequence associated with it, the enhancer and promoter regions, has to be of a certain minimum length and the sequence unique and specific, otherwise you might get unlucky and the regulator protein will bind somewhere else in the genome that looks too much like this gene's enhancer and promoter region. The result of which might either be that you accidentally shut off some vital gene, or that the one you want turned on to digest your carbohydrate, doesn't get turned on.

Now the thing is, different genes have different enhancer/promoter regions for obvious reasons just touched upon. So these enhancers and promoters just have to be sufficiently different from each other that they eliminate, or at least sufficiently reduce "noisy regulation" to levels so low it doesn't otherwise interfere with normal organismal function.

What this also means is that, once you've designed your requisite organism as we postulate you did, supernatural designer as you are. You can in principle design in some complete set of different enhancer and promoter regions and associated regulatory proteins that you don't have to change ever again, because you've made enough of them, and made sure they're different enough from each other, that you avoid interering levels of noisy transcription.

That means there's an possible fits-all complete set of enhancer-promoter regions you could just re-use and re-use over and over again in all lifeforms you create. No reasons to change them and their associated binding regulatory proteins at all because, remember, they just have to prevent levels of cross-talk so high they interfere with normal organismal function.

You make your first organism with a lot of genes, maybe 25.000 protein coding genes with thousands and thousands of unique promoter and enhancer regions that fit all their requisite genes, and then you're done. You can keep re-using these "switches" in all the life you subsequently create without having to change them, you've already made them different enough that they prevent unwanted cross-talk.

But fuck me, while we do observe similarities between these regions and their associated regulatory proteins, they still do in fact change slowly over inferred evolutionary time. While closely related species have very similar such enhancer and promoter regions (some of them are almost completely conserved throughout, for example, all mammals), once we get further and further out, they still do slowly change. They accumulate NEUTRAL/SILENT mutations, which fall into nested hierarchies.

This thing about neutral/silent is particularly important, because we might have argued that these changes are due to physiological constraints, such that only a specific promoter sequence or regulatory protein would work in a specific single species. However, if we can change these sites according to well-known mutational biases and still get a functional regulatory element, we strong reasons not to think regulatory elements are significantly physiologically constrained in general.

So, let's test that claim!
Here's a paper where the authors are trying to reconstruct some key events in archeal evolution. What the authors are trying to establish is really besides my point, so we don't have to bother with much of the contents of the paper, what we're looking for is a maximum likelihood tree constructed using an archeal flagellum regulatory protein:

A key cellular structure that, judging from the genome sequence, is present in Nst1 but not in N. equitans is the archaeal flagellum (archaellum) [18]. Genes encoding all the essential subunits of the archaellum have been identified (Figure 5), including two archaeal flagellins and the gene responsible for flagellar assembly, function and regulation (flaD/E,F,G,H,I,J, FleN). The presence of the flaD/E gene, so far only identified in Euryarchaeota, and the topology of the phylogenetic tree of the regulatory subunit flaH (Additional file 5) are compatible with a euryarchaeal type-archaellum in Nst1.

So the flagellum of Archea has a key regulatory element, a protein that binds a specific DNA sequence in the Archaeal genome and initiates flagellar biosynthesis.

This shows the phylogentic tree which results from alignments of the Archaeal protein FlaH, which is involved in regulation of Archaeal flagellum synthesis. The data we need are the protein names. Pick a protein on the list, like "229583692 Sulfolobus islandicusM 16 27 uid58851" and do a pubmed search for the protein sequence, this gives us the following protein amino acid sequence:
http://www.ncbi.nlm.nih.gov/protein/229583692

ORIGIN
1 megctviikt gnedldrrls gipfpalimi egdhgtgksv lsaqfcygll iggkkgyvit
61 teqtskdylk kmkdvkinli pfflkgvlgi aplntnrfnw nstlankile viidfikkrk
121 nmnfviidsl sivatfaeik qilqfmkdar vlvdlgklil ftvhpdvfne elksritsiv
181 dvyfklsats iggrrikvle riktiggiqg adaisfdidp algvkvvpls lsra
//

Then just pick a distantly related one on the other end of the tree from another Archaea species, "222480972 Halorubrum lacusprofundi ATCC 49239 uid58807":

ORIGIN
1 mphdnllslg lgerdrlnke lgggiprgsi vlmegdygag ksaisqrfay glveegasvt
61 vmsteltvrg fidqmhsley dmvkpllqee llflhadfds ggafsdddge rkellkrlmn
121 aeamwnsdvi fldtfdaifr ndptfealvr kneerqaale iisffreiis qgkvvvltvd
181 psavdddaig pfrsiadvfl qlemievgnd irrqinvkrf agmgeqvgdt igfsvrsgtg
241 iviesrsva
//

Producing alignment with these two protein sequences using http://blast.ncbi.nlm.nih.gov/Blast.cgi gets us this result:

Which shows that these two arbitrarily picked regulatory proteins (FlaH, a flagellum related regulatory element) that performs the same function in two distantly related Archaea, differ in their amino acid sequence by as much as 77%. Almost the entire protein has changed, in fact the sequence identity is so low it is approaching the limit at which we think we can infer homology due to sequence identity, yet it still works just as well regulating Archaea flagellar biosynthesis.

That means that the only constraint we are evidentially justified in inferring operates on regulatory sequence is a sufficiently large sequence to distinguish it from other regulatory regions to make it sufficiently improbable for random mutations to induce unwanted noisy crosstalk/transcription.

 

[DutchLiam84]

I think he buggered off.

 

[Rumraket]

Well, I have been kinda busy with other stuff, not having had the time to dig into this crap until now.

Oh well, no reason not to develop the arguments for common descent and really make all the many underlying peculiarities and rationales more explicit, and show exactly why the usual ID catch-phrase "common design" doesn't actually explain the observed pattern at all.

All they have is ad-hoc reasoning to a designer never observed.

 

[Dragan Glas]

Greetings,

Interesting article which touches on this topic - Novel Genetic Patterns May Make Us Rethink Biology and Individuality:

Because somatic changes are thought to happen at random, scientists do not expect unrelated people to exhibit the same mutations. Williams and colleagues analyzed the same 10 tissue samples in two unrelated people. They found several identical mutations, and detected these repeated mutations only in kidney, liver and skeletal body tissues. Their research examined "mitochondrial DNA" (mtDNA) -- a part of DNA that is only inherited from the mother. Technically all women would share mtDNA from one common female ancestor, but mutations have resulted in differences. The importance of Williams' finding is that these tissue-specific, recurrent, common mutations in mtDNA among unrelated study subjects -- only detected in three body tissues -- are "not likely being developed and maintained through purely random processes," according to Williams. They indicate "a completely different model …. a decidedly non-random process that results in particular mutations, but only in specific tissues."

If our human DNA changes, or mutates, in patterns, rather than randomly; if such mutations "match" among unrelated people; or if genetic changes happen only in part of the body of one individual, what does this mean for our understanding of what it means to be human? How may it impact our medical care, cancer screening, or treatment of disease? We don't yet know, but ongoing research may help reveal the answers.

Essentially, this is a intra-species example of finding similarities across different species (phylogenetic trees).

Which should not be a surprise as evolution is essentially mutations within a species eventually resulting in a new species.

Kindest regards,

James

 

[he_who_is_nobody]

Here we have a small list of none other than ID proponents and Creationists affirming exactly this claim:

CREATIONISTS and Intelligent Design proponents themselves have stated clearly that every and all mutations are CATASTROPHIC. Remember that? "Catastrophic."

Every human baby born has somewhere between 100 to 200 more mutations than its parents (depending on how you count)-- and twice that number relative to its grandparents-- and thrice that relative to its great-grandparents-- etc.

Young Earth Creationist Kent Hovind: “A change of only three [DNA] nucleotides is fatal to an animal. There is no possibility of [genetic] change.” (Ken Hovind, Source: http://media.drdino.com/sem/audio/mp3/books2.mp3 @ 82:10, March 2003, cited at http://kent-hovind.com/quotes/sciencei.htm)

Got that? Kent Hovind says only three mutations will kill an animal.

If creationism is correct, every baby has 100 to 200 new CATASTROPHES its parents didn't have-- and twice that number of CATASTROPHES relative to its grandparents-- and thrice that relative to its great-grandparents-- etc. Enough to kill every baby on Earth a hundred times over.

Pro-ID Philosopher William Dembski: “[T]here is now mounting evidence of biological systems for which any slight modification does not merely destroy the system’s existing function but also destroys the possibility of any function of the system whatsoever.” [Dembski, The Design Revolution, p. 113]

Pro-ID lawyer Phillip Johnson: “Biologists affiliated with the Intelligent Design movement nail down the distinction by showing that DNA mutations…make birth defects” ["Berkeley's Radical: An Interview with Phillip E. Johnson", November 2000.]

Pro-ID lawyer Edward Sisson: “[T]he theory of unintelligent evolution, which depends entirely on the supposed occurrence in history of trillions of DNA mutations that beneficially affect body shape, has not identified any such mutations” -- [Edward Sisson, “Darwin or Lose”, Touchstone, v. 17, issue 6, July/Aug. 2004]

Uncommon Descent: “As far as I know, the current consensus of population geneticists is that mutations do indeed have disastrously bad fitness.” [Eric Holloway. Uncommon Descent. August 28, 2011.]

Young Earth Creationist Henry Morris: “Inheritable and novel changes (mutations) which take place in organisms today have always been observed to be harmful.” [Henry Morris, The Remarkable Birth of Planet Earth, p.vii]

Young Earth Creationist Duane Gish: “the mutations we see occurring spontaneously in nature or that can be induced in the laboratory always prove to be harmful.” [Gish, Evolution? The Fossils Say No, p. 47]

Duane Gish: “all mutations are bad” [Gish, Dinosaurs by Design (1992), p.83]

Duane Gish: “Remember, all the changes were just mistakes, they were genetic errors, mutations, almost everything which is bad… they're all bad” [Keith Saladin-Duan Gish Debate II, 1988]

Creationist Don Boys: “Not only are mutations always harmful, but they produce changes in present characters, never producing new characters. Mutations are the catalyst for defects, deformity, disease, and death; yet evolutionists scream that they are the explanation for all the varieties we see… [T]he results of all mutations: disorder, defects, disease, deformity, and death.” -- ["Almost a Thousand Major Scientists Dissent from Darwin!", Don Boys. Canada Free Press. May 2, 2010.]

Muslim Creationist Harun Yahya: “[N]ot one single useful mutation has ever been observed… The slightest alteration in [genetic] information only leads to harm.”

The Muslim creationist sex-cult of Harun Yahya says all mutations cause only harm: “Mutations… like all accidents, they cause harm and destruction. The changes effected by mutations can only be like those experienced by people at Hiroshima, Nagasaki, Chernobyl … freaks of nature… because all efficient(?) observable mutations cause only harm to living things.”

There we have it. All the creationist top dogs and professional ID proponents of the discovery institute go out of their ways to tell us that introducing mutations to extant functional DNA and proteins will invariably always lead to loss of function and dead sequences. Mutation just cannot create anything new that works. This is their claim.

Wow. Thank you for this. I have a feeling a list like this will come in handy.

 

[Rumraket]

Heh, yes, that list really does make a complete mockery of ID and creationism in all their forms. Those people quoted are the top dogs of the creationism and ID think tanks, their "experts", their "scientists".

It's really their most important argument, the one all their objections to evolution eventually reduces to. To them it's not just that evolution didn't happen, it's that it supposedly can't. To argue this, they have to try to paint a picture where even tiny genetic changes "breaks" gods superiorly fine-tuned creations.

And there they are, spewing demonstrable falsehoods. All of it, every single word in that entire list, is refuted by that single last citation I gave about the Archaeal flagellum regulatory element. It can be pretty much mutated indiscriminately and you still get a functional regulatory element.

This puts lifepsyops in a bit of a conondrum because, either he would have to side with the professional ID-proponents and top-dog creationists engange in blanket denial of observational reality, in which case he then strengthens the argument for the validity of the inference from ancestral sequence reconstruction

or

- he accepts that huge amounts of genetic changes are a demonstrable possibility (and therefore that all the creationists and professional ID-proponents are wrong), in which case he doesn't have a valid argument for why evolution couldn't happen.

Almost a shame he's gone, would have liked to see him try to squirm out of that one.

 

[Deleted member 619]

Some absolutely outstanding work in this thread by Rum.

It should be said that you've attained a quite scary standard in the time we've known each other. Truly one of the big hitters now, and for some time.