Coyne's review of Behe's new book on Darwinism

Rumraket · **#141** by **Rumraket** » Apr 16, 2020 4:55 pm

Wortfish wrote:
Rumraket wrote:
Ahh the "specific / peculiar compotent" as opposed to the "generic" one. What the hell does that mean? Either two components work together or they do not. Some times they do, and when they do, natural selection can favor that association.

By specific/peculiar, I mean a component that is new, not something recruited from an existing inventory.

And you have not defined new. Creationist propagandists never do that. So I have decided to do it for them:
The one fits-all definition of “new” for use in evolutionary biology:
If it’s different from what it was before, then it’s new(QED).

If it’s slightly bigger, slightly smaller, slightly darker, slightly longer, slightly thinner, slightly more curved, if it has changed in ANY measurable way, then it’s new. That goes for physiological, mental, behavioral, and molecular changes of any and all kinds, whether in quality or quantity. Changing a T nucleotide into a G nucleotide is change, and therefore new. An ever so slightly taller person is different, so also new. Gene duplication means there is now more genes than before, so it’s different form what it was before, therefore also new.

There we go, “new” has now been defined and any measurable change now qualifies as new.

With respect to new information: New information is any change in a sequence such as a polymer like DNA, or amino acids, or a string of abstract symbols used in writing (including it’s length, or the order of arrangement of monomers or symbols within it) that wasn’t there before. If it wasn’t there before, it’s new. So any mutation is new information. All duplications are new information. All substitutions are new information. All deletions are new information, because they all constitute change that wasn’t there before.

Using this simple, intuitive definition of what would be “new”, all mutations cause new information and new functions.

So now any mutation that results in a changed protein coding gene is now a new protein. A duplication of an already existing protein coding gene is a new protein. A mutation of a noncoding region that previously did not yield a protein molecule with a function being retained by natural selection, that renders said noncoding region produce a protein molecule with a beneficial function, is a new protein and new genetic information.

Wortfish wrote:
Rumraket wrote:Yeah some of them do this just by themselves. Some proteins will naturally oligomerize into structures like pentamers, hexamers, octamers or what have you. Naturally oligomerizing structures, created by a single protein all by itself. A single protein coding gene is expressed continously, and as the number of proteins build up they self-assemble into larger structures. Good examples are evolution of beta-propeller structures. A bona fide molecular machine that evolved.

You can't seriously claim that the bacterial flagellum, or eukaryotic cilium, are just a bunch of proteins thrown together.

I didn't you dyslexic ghoul.

The bacterial flagellum and eukaryotic cilium are both examples of molecular machines that essentially constitute "a bunch of proteins" most of which first evolved by mutation and natural selection for other functions, and which later were coopted to perform functions in ancestors of both of these contemporary molecular machines.

Nobody is saying there was a huge collection of proteins that were just randomly thrown together until it happened to produce a flagellum. Read Matzke 2003.

Wortfish wrote:
Rather, both represent a "purposeful arrangement of parts" that produce a specific function...i.e. design rather than random assemblage.

Except that calling it a "purposeful arrangement of parts" is begging the question. And the appearance of a purposeful arrangement of parts is exactly what natural selection produces, so detecting the mere appearance of a "purposeful arrangement of parts" can't be an indication of design when there is a well-established non-design mechanism know to produce the same results. Since the molecular machines of life are made of evolvable entities(proteins) encoded in the genomes of evolving populations of organisms, and since their evolutionary history can be elucidated with phylogenetic methods, the best supported conclusion we can draw from the evidence is that they evolved.

Wortfish · **#142** by **Wortfish** » Apr 16, 2020 11:32 pm

Spearthrower wrote:
I expressly told you in the post you're supposedly replying to what I did: I typed 'evolution of the vertebrate eye' into Google Scholar to verify your inane assertion that there are no papers at all on the evolution of the vertebrate eye, and lo and behold there are 151,000 papers... how many of them have you read, Wortfish?

151,000 is not 'zero' - ergo, your mindless blather is debunked.

This is ridiculous. Of course, there are many papers on the hypothetical evolution of the eye. Most consider phenotypic changes, some possible genetic ones. But there isn't a single paper out there which can provide a clear account of how the eye purportedly evolved through random mutation and natural selection, revealing the exact changes that occurred, in what genes, and what the fitness effect of this was.

So, factually, despite you claiming that no scientist can show how the vertebrate eye evolved, the paper does exactly that - your wibble and distraction about existing eyes is completely irrelevant as you never specified that it had to be generated from nothing ala Creationist Pokemon evolution.

No. Here again, no scientist can claim to know the exact variations that took place, although the phenotypic picture may be easier to imagine.

Grab a hold of them goalposts. No one has ever said that the vertebrate eye evolved from a single nerve cell - that would be mentally deranged bollocks contrived in abject fucking ignorance considering the ancestors of vertebrates already had eyes, and vertebrates consequently possessed eyes from the moment they first evolved. Those eyes themselves adapted over generations, but no one is going to argue that vertebrates evolved absent vision.

Right. But the vertebrate eye purportedly evolved from an invertebrate eye which did evolve from a single nerve cell. That requires a lot of explaining!

Mivart's completely irrelevant to everything. We don't need to discuss the discussion of theorists 150 years ago when those people were unarguably absent possession of the wealth of empirical evidence we have today.

No. Because the incipient stages in the development of a new structure are always problematic as they confer little or no benefit and may even be harmful This is what the late SJ Gould had to say about Mivart: https://philpapers.org/rec/GOUNNA

One point stands high above the rest: the dilemma of incipient stages. Mivart identified this problem as primary and it remains so today.

And as I and others have already explained to you - a single photosensitive spot already confers a benefit not possessed by organisms lacking said photosensitive spot. It doesn't matter if that benefit is miniscule - it would still offer the ability to detect potential danger from further away and confer the ability to evade predation with less risk of harm than via chemical or mechanical sense.

It does matter, because if the benefit is negligible then the change is likely to be lost to random drift. The presence/absence of light need not be due to the presence or absence of a predator. It could be prey. It could be a whole number of things. And, even then, the response may be insignificant. And even to get to that stage requires changes to genes and their regulation.

In summary;

1. You are lying.
2. You don't know what you're talking about.
3. Your arguments are appeals to incredulity/ignorance.
4. 151,000 papers for you to get through before you can make any claims about what can or can't be explained - run along now and come back when you're finished.
5. You're a propagandist for ideology, unable to provide any support for your belief system, you instead opt for the typical fundamentalist Creationist fallacy of trying to attack science as if - were you able to disprove it - that would make your fantastical belief system the last man standing. Of course, your attempts are laughable because you simply do not possess any relevant knowledge or ability - Creationist hubris makes you believe that you can overturn empirical facts by strength of ideological conviction, whereas in the real world, everyone just considers you and your ilk clowns.

You haven't read 151,000 papers on the subject. In any case, there are thousands of papers about extraterrestrial life. It doesn't mean that we have any evidence for ETs or we should believe they exist on other planets: https://scholar.google.com/scholar?hl=e ... e%22&btnG=

There are even more papers on unicorns for goodness sake!: https://scholar.google.com/scholar?hl=e ... s%22&btnG=

Wortfish · **#143** by **Wortfish** » Apr 16, 2020 11:59 pm

Rumraket wrote:
I didn't you dyslexic ghoul.

I think you may have meant fool. But anyway....

The bacterial flagellum and eukaryotic cilium are both examples of molecular machines that essentially constitute "a bunch of proteins" most of which first evolved by mutation and natural selection for other functions, and which later were coopted to perform functions in ancestors of both of these contemporary molecular machines.

Nobody is saying there was a huge collection of proteins that were just randomly thrown together until it happened to produce a flagellum. Read Matzke 2003.

I am glad you mentioned the idea of co-option, or exaptation. The big flaw in believing, for example, that the base of the bacterial flagellum was a Type-3 secretory system (in the past) is that evolutionary trajectories are not so flexible and reversible. Something going down one path isn't going to head down a totally different one.

Indeed, the only way for a secretory system to evolve into a propulsion system would be to stop its secretory function entirely, at which point it would be good for nothing.

We hear this silly argument a lot, such as with feathers. Initially, they were for just for thermal regulation and then got re-purposed for flight also. However, that is a misinterpretation. Many organs and structures - and also genes - have a dual function.

laklak · **#144** by **laklak** » Apr 17, 2020 12:45 am

Lol. YOUR explanation is so much better, eh?

Cmon, let's see all those peer reviewed papers that explain how Sky Daddy magicked it all. Show your work. Sauce for ganders and such like.

Lol again.

Hermit · **#145** by **Hermit** » Apr 17, 2020 12:49 am

Wortfish wrote:But there isn't a single paper out there which can provide a clear account of how the eye purportedly evolved through random mutation and natural selection, revealing the exact changes that occurred, in what genes, and what the fitness effect of this was.

It's amazing how many people have more trouble believing in a process, namely evolution, we have plenty of evidence for than the agency of an invisible agency.

I wish you'd go back to egregious quote mining with which you attempt to show that an author has meant the opposite of what he has in fact meant. It may be fraudulent, yes, but it is way more entertaining than yet another recitation of bog standard creationist canards.

Hermit · **#146** by **Hermit** » Apr 17, 2020 12:58 am

laklak wrote:Lol. YOUR explanation is so much better, eh?

Cmon, let's see all those peer reviewed papers that explain how Sky Daddy magicked it all. Show your work. Sauce for ganders and such like.

Lol again.

Once upon a time two explorers came upon a clearing in the jungle. In the clearing were growing many flowers and many weeds. One explorer says, "Some gardener must tend this plot." The other disagrees, "There is no gardener." So they pitch their tents and set a watch. No gardener is ever seen. "But perhaps he is an invisible gardener." So they set up a barbed-wire fence. They electrify it. They patrol with bloodhounds. (For they remember how H. G. Well's The Invisible Man could be both smelt and touched though he could not be seen.) But no shrieks ever suggest that some intruder has received a shock. No movements of the wire ever betray an invisible climber. The bloodhounds never give cry. Yet still the Believer is not convinced. "But there is a gardener, invisible, intangible, insensible to electric shocks, a gardener who has no scent and makes no sound, a gardener who comes secretly to look after the garden which he loves." At last the Skeptic despairs, "But what remains of your original assertion? Just how does what you call an invisible, intangible, eternally elusive gardener differ from an imaginary gardener or even from no gardener at all?" ~ John Wisdom

campermon · **#147** by **campermon** » Apr 17, 2020 7:52 am

Wortfish wrote:

I am glad you mentioned the idea of co-option, or exaptation. The big flaw in believing, for example, that the base of the bacterial flagellum was a Type-3 secretory system (in the past) is that evolutionary trajectories are not so flexible and reversible. Something going down one path isn't going to head down a totally different one.

What is the explanation for their similarity?

theropod_V_2.0 · **#148** by **theropod_V_2.0** » Apr 17, 2020 8:14 am

campermon wrote:
Wortfish wrote:

I am glad you mentioned the idea of co-option, or exaptation. The big flaw in believing, for example, that the base of the bacterial flagellum was a Type-3 secretory system (in the past) is that evolutionary trajectories are not so flexible and reversible. Something going down one path isn't going to head down a totally different one.

What is the explanation for their similarity?

Simple. The grand designer is a short order cook, like a “chef” at a Waffle House. He only needs to know how to break an egg.

RS

ETA: Yeah, it’s 3 am and I’m having a little trouble sleeping for some reason.

campermon · **#149** by **campermon** » Apr 17, 2020 8:36 am

theropod_V_2.0 wrote:
campermon wrote:
Wortfish wrote:

I am glad you mentioned the idea of co-option, or exaptation. The big flaw in believing, for example, that the base of the bacterial flagellum was a Type-3 secretory system (in the past) is that evolutionary trajectories are not so flexible and reversible. Something going down one path isn't going to head down a totally different one.

What is the explanation for their similarity?

Simple. The grand designer is a short order cook, like a “chef” at a Waffle House. He only needs to know how to break an egg.

RS

ETA: Yeah, it’s 3 am and I’m having a little trouble sleeping for some reason.

Rumraket · **#150** by **Rumraket** » Apr 17, 2020 9:51 am

Wortfish wrote:
Rumraket wrote:
I didn't you dyslexic ghoul.

I think you may have meant fool.

Uhm, okay. If it makes you feel better.

Wortfish wrote:
Rumraket wrote:The bacterial flagellum and eukaryotic cilium are both examples of molecular machines that essentially constitute "a bunch of proteins" most of which first evolved by mutation and natural selection for other functions, and which later were coopted to perform functions in ancestors of both of these contemporary molecular machines.

Nobody is saying there was a huge collection of proteins that were just randomly thrown together until it happened to produce a flagellum. Read Matzke 2003.

I am glad you mentioned the idea of co-option, or exaptation. The big flaw in believing, for example, that the base of the bacterial flagellum was a Type-3 secretory system (in the past) is that evolutionary trajectories are not so flexible and reversible.

Your claim about a flaw is nothing but a bare assertion in contradiction to the evidence. We know the two structures are related because there is significant nesting hierarchical structure in the sequences of proteins of which they are made, and phylogenetic trees derived from different components show a high degree of consilience. In addition to the fact that they're essentially identical in structure and function.

Wortfish wrote:
Something going down one path isn't going to head down a totally different one.

Another bare assertion. Look, this argument is completely meaningless if all you're ever going to do is just brainlessly declare that X is so without ever doing any work to show that the claim is true.

By the way, the T3SS analogue in the flagellum still functions as a protein secretion system. It is responsible for secreting the proteins that make up the rod, hook, and filament. Type III secretion systems: the bacterial flagellum and the injectisome

"Although these two machineries clearly differ both in overall structure and function, at their core, they both consist of a conserved machinery for protein export, the type III secretion system (T3SS). In the flagellum, the T3SS is used to export the distal flagellar components and build the extracellular filament."

Wortfish wrote:Indeed, the only way for a secretory system to evolve into a propulsion system would be to stop its secretory function entirely

Bzzzzt. Wrong. The flagellar T3SS still functions as a protein secretion system. There is no reason to think it ever stopped doing so before it was exporting flagellar proteins but something else related instead.

Wortfish wrote:
We hear this silly argument a lot, such as with feathers. Initially, they were for just for thermal regulation and then got re-purposed for flight also. However, that is a misinterpretation.

No, that's actually the best explanation for the historical pattern implied by the fossil record.

theropod_V_2.0 · **#151** by **theropod_V_2.0** » Apr 17, 2020 10:17 am

Sexual selection also may have played a big role in not just in preservation, but also in diversity, of feathers in most, if not all, dinosaurs. This is why I suggested Wartface lower himself to read my thread about how we KNOW all birds are the direct descendants of maniraptoran theropod dinosaurs. Thermoregulation in brooding clutches of eggs, and prey acquisition, probably also played their parts. Flight was most likely a secondary adaptation arising from a combination of all the above.

Yes, I know, I have bastardized a member’s user name, but the blatant bullshit tactics have earned a complete loss of respect. I still feel there is a good deal of trolling taking place, or well crafted Poe playing, with our supposed creotard/ID hero.

RS

Wortfish · **#152** by **Wortfish** » May 03, 2020 10:08 am

Rumraket wrote:
By the way, the T3SS analogue in the flagellum still functions as a protein secretion system. It is responsible for secreting the proteins that make up the rod, hook, and filament. Type III secretion systems: the bacterial flagellum and the injectisome

Point taken. The base of the flagellum is indeed used for the export of proteins used in the structure's assembly: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183434/

However, this differs completely from the function of the secretion system of the injectisome that some claim is a derivation of the flagellum and not a precursor to it. Just because two structures use the same part doesn't mean that they are related. The point still stands about evolutionary trajectories and the problem of going down an entirely different route. The injectisome secretes proteins used in bacterial infection of their hosts. This capability would have been lost had the secretory system been re-tooled for use exporting proteins for components of a locomotion system whose design had not hitherto been completed.

Wortfish · **#153** by **Wortfish** » May 03, 2020 10:09 am

theropod_V_2.0 wrote:Sexual selection also may have played a big role in not just in preservation, but also in diversity, of feathers in most, if not all, dinosaurs. This is why I suggested Wartface lower himself to read my thread about how we KNOW all birds are the direct descendants of maniraptoran theropod dinosaurs. Thermoregulation in brooding clutches of eggs, and prey acquisition, probably also played their parts. Flight was most likely a secondary adaptation arising from a combination of all the above.

Yes, I know, I have bastardized a member’s user name, but the blatant bullshit tactics have earned a complete loss of respect. I still feel there is a good deal of trolling taking place, or well crafted Poe playing, with our supposed creotard/ID hero.

RS

What, in your view, was the incipient stage in feather development? An epidermal depression?

Wortfish · **#154** by **Wortfish** » May 03, 2020 11:06 am

laklak wrote:Lol. YOUR explanation is so much better, eh?

Cmon, let's see all those peer reviewed papers that explain how Sky Daddy magicked it all. Show your work. Sauce for ganders and such like.

Lol again.

I will refer you to this research on the eye: Simple Eyes Of Only Two Cells Guide Marine Zooplankton To The Light
https://www.sciencedaily.com/releases/2 ... 140705.htm

The simplest of all eyes, on the larvae of marine ragworms, consist of just two cells. They are a photoreceptor cell and a pigment cell that confers the directional sensitivity to light. It absorbs light and casts a shadow over the photoreceptor. The larvae can sense both the presence and rough direction of light that allows for their movement towards light (i.e phototaxis).

However, crucial to all this is the nerve connecting the photorecptor to the cilia:

The scientists found that a nerve connects the photoreceptor cell of the eyespot and the cells that bring about the swimming motion of the larvae. The photoreceptor detects light and converts it into an electrical signal that travels down its neural projection, which makes a connection with a band of cells endowed with cilia. These cilia - thin, hair-like projections - beat to displace water and bring about movement.

This confirms my own understanding:

1. An eye requires more than just a photoreceptor. It needs another cell to detect the direction of the source of light.
2. A nerve must connect the photorecptor to a locomotive apparatus, like the cilium, to permit a reflex action in response.

If these were not present, then a single photoreceptor would not itself have been useful enough to be preserved.

theropod_V_2.0 · **#155** by **theropod_V_2.0** » May 03, 2020 12:24 pm

Read.
The.
Thread.
Wortfish.

RS

Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

Re: Coyne's review of Behe's new book on Darwinism

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