New genes required for the Cambrian explosion

[lee_merrill]

There will always be questions. That's why scientists keep examining things and reexamining them. As they say the most exciting thing to hear is "I don't know" followed by "let's see if we can find out why/how"

Yes, and let's follow the evidence wherever it leads, yes? Even if it leads to design...

Blessings,
Lee

[lee_merrill]

In the end they found that the complete evolution of an eye like those found in a vertebrate or octopus took less than 2000 steps.

So what is a rough probability of each step? .9 ^2000 is about 3 x 10^-92

Lee, I recommend these rather than dredging through sources that have repeatedly shown to have lied to you.

Well, I believed Behe was wrong, after reading "Finding Darwin's God" by Miller, until I read Behe's book! Thinking "it's at least of historical interest, even if he's been refuted." Speaking of being lied to.

Blessings,
Lee

[lee_merrill]

No, i'm saying far more than 150. One species has 169 genes that aren't present in other species, another has 253. There are also over 150 genes present in all drosophila species that aren't present in other fly genera, some of which undoubtedly post-date the splits 15 million years ago.

Well, how many post-date the split? I'm trying to get an idea of the rate of new genes.

And, as always, you have no evidence to support your claims. Not that you've defined things like "sufficient" in any way that can be addressed with evidence.

So you are saying there is no reason to suppose that generation of subnetworks would be more difficult?

By not saying "true" to these two, you come across as someone in denial of basic reality.

No, I want to know what's true, and I find your counterarguments have counters to them.

Blessings,
Lee

[rogue06]

Yes, and let's follow the evidence wherever it leads, yes? Even if it leads to design...

Blessings,
Lee

I'm a big time believer in following the evidence. It was what dragged me kicking and screaming in to accepting evolution. I didn't want to accept it. I didn't like it. I preferred my Old Earth Creationist roots. But all of the cross-correlating, corroborating, consilient positive evidence from dozens of different and independent scientific disciplines that that quite literally continues to amass on a daily basis made it impossible.

Basically, any time you have imperfect self-replicators in an environment of limited resources, the result is going to be a tendency of those best suited to acquire and use the resources to produce more offspring.

This will continue to happen again and again, over and over as life changes and adapts to its environment

Furthermore, no means has ever been observed that would ever prevent numerous small changes from accumulating into larger scale changes over scores of generations.

Evolution is about what happens to life after it arose, regardless of how it arose. It matters not a whit if life came about through purely naturalistic means or was zapped into existence ex nihilo. Either way, evolution still works.



Okay, enough speechifying. Back to following the evidence

This view has been expressed repeatedly by legitimate scientists. For instance:

• "If a man will begin with certainties, he shall end in doubts; but if he will be content to begin with doubts, he shall end in certainties." --Francis Bacon in Book I of The Advancement of Learning 1605
• "I keep my theories on the tips of my fingers so that the merest breath of fact can blow them away." --Michael Faraday
• "I have steadily endeavored to keep my mind free so as to give up any hypothesis, however much beloved, as soon as the facts are opposed to it." --Charles Darwin (who also wrote: "A scientific man ought to have no wishes, no affections - a mere heart of stone.")
• "Sit down before a fact as a little child, be prepared to give up every preconceived notion, follow humbly wherever and to whatever abysses nature leads, or you shall learn nothing." --Thomas Henry Huxley
• "The hallmark of science is not the question 'Do I wish to believe this?' but the question 'What is the evidence?' It is this demand for evidence, this habit of cultivated skepticism, that is most characteristic of the scientific way of thought." --Douglas Futuyma
• "A scientist should every morning eat one of his favorite theories for breakfast." --Konrad Lorenz
• "Any real systematist [or scientist in general] has to be ready to heave all that he or she believes in, consider it crap, and move on, in the face of new evidence." --Mark Norell (in his Unearthing the Dragon)
• "In science it often happens that scientists say, 'You know that's a really good argument; my position is mistaken,' and then they would actually change their minds and you never hear that old view from them again. They really do it. It doesn't happen as often as it should, because scientists are human and change is sometimes painful. But it happens every day."^[1] --Carl Sagan

And that is by and large what happens.^[2]

Not too long ago, after the discovery of a 14 myo fossil of a type of honey bee in North America Michael Engel of the University of Kansas and co-author of Evolution of the Insects excitedly said "I got to overturn some of my own stuff"

Donald Prothero in his book Evolution: What the Fossils Say and Why It Matters cites a couple examples of just such occurrences taking place, such as with the issue of continental drift and plate tectonics. He notes that, "'The Old Guard' who had a lot of time and research invested in fixed continents tended to be skeptical the longest, and many held out until the evidence became overwhelming. Eventually, they all had to concede their cherished beliefs were wrong."

Prothero revealed how the famous geologist Marshall Kay, who had spent his entire life explaining the complexities of geology based on the assumption that continents did not move (even publishing a major book on the topic), ended up embracing plate tectonics when the evidence for it started to amass. Even though he was near retirement age Kay began redoing his life's work using the new concepts and his work ended up providing a good deal of the geological evidence used in support of the theory.

And everybody's favorite Richard Dawkins has over the years repeatedly recounted one instance that he had witnessed:

I have previously told the story of a respected elder statesman of the Zoology Department at Oxford when I was an undergraduate. For years he had passionately believed, and taught, that the Golgi Apparatus (a microscopic feature of the interior of cells) was not real: an artifact, an illusion. Every Monday afternoon it was the custom for the whole department to listen to a research talk by a visiting lecturer. One Monday, the visitor was an American cell biologist who presented completely convincing evidence that the Golgi Apparatus was real. At the end of the lecture, the old man strode to the front of the hall, shook the American by the hand and said -- with passion -- "My dear fellow, I wish to thank you. I have been wrong these fifteen years." We clapped our hands red.

I can continue giving example after example of this including debates over whether humans were in the Americas prior to the Clovis culture; the megaflood in eastern Washington that resulted in the formation of the Scablands; how a champion of the idea that whales arose from mesonychids abruptly changed his mind and agreed they actually arose from artiodactyls (an idea he had adamantly opposed) when he discovered a bone that contradicted his presumptions.

And yes I can include examples specifically relating to evolution.

There have been numerous examples of what were initially considered to be controversial theories (as they accounted for observed biological changes that did not correspond to the expectations of the neo-Darwinian models derived from the New Synthesis -- which itself over-turned pure Darwinian thought and theory -- that was developed in the mid 1930s through the mid 40s) that have been accepted.

• Like when Conrad Waddington proposed developmental evolution (evo-devo) in 1942

• Like when Willi Hennig proposed phylogenetic systematics (cladistics) in 1950

• Like when Motoo Kimura proposed the neutral theory of molecular evolution (genetic drift) in 1968

• Like when Lynn Margulis proposed Endosymbiotic theory in 1970

• Like when Niles Eldredge and Stephen Jay Gould proposed punctuated equilibrium in 1973

• Like when Sřren Lřvtrup proposed Epigenetics in 1974

• Like when Carl Woese proposed horizontal gene transfer in 1977

What none of the scientists who initially opposed any of the above mentioned items ever did was automatically reject the evidence that showed that their cherished ideas had been mistaken. They didn't dismiss it because they had signed an oath demanding that they unconditionally dismiss any and everything that didn't support what they had already concluded. And they certainly didn't throw a hissy fit and threaten those who questioned them with going to hell for daring to disagree as YEC John Baumgardner did as he ran off during a discussion about the RATE (Radioisotopes and the Age of The Earth) project with Kirk Bertsche and several others after just a few exchanges here at Tweb several years back^[3].

Oops. I started speechifying again






1. As Sagan notes it doesn't happen enough and I'll add that there will always be holdouts but in general science advances when new information demonstrates an old view does not reflect reality. If it didn't we would still think that the earth was immobile and the sun revolved around it or the elements consist of air, earth, fire and water.

2. And it's why I detest claims of "settled science" All science is provisional. It should always leave room for the possibility, no matter how small, that some new discovery could come along an upset the apple cart. That being said, the Theory of Evolution is perhaps the most tested of all scientific theories and it has never once been shown wanting.

3. One could also look at the difference in the replies that Bill Nye and YEC leader Ken Ham provided during their debate a few years ago when each was asked if there is anything that could get them to change their mind. Nye responded that evidence could whereas Ham intoned that nothing could.

[TheLurch]

Well, how many post-date the split? I'm trying to get an idea of the rate of new genes.

A minimum of 422 post date the split, plus the drosophila specific ones that are present in all genera.

So you are saying there is no reason to suppose that generation of subnetworks would be more difficult?

I only know of subnetworks in terms of ethernet. Maybe you can clarify that.

No, I want to know what's true, and I find your counterarguments have counters to them.

Yes, if you don't care about the quality of the arguments, there are always counters.

You've not addressed the fact that we have actual worm tracks leading to actual worms in Ediacaran deposits. Ergo, bilaterians necessarily predate the Cambrian. What part of that don't you get?

[lee_merrill]

I'm a big time believer in following the evidence. It was what dragged me kicking and screaming in to accepting evolution.

Thank you for your considered reply. It's the evidence that has me believing that a designer is necessary to account for all the complexity we see.

Furthermore, no means has ever been observed that would ever prevent numerous small changes from accumulating into larger scale changes over scores of generations.

Irreducible complexity? May I ask if you have read one of Behe's books? I've read The Beak of the Finch and Finding Darwin's God.

One could also look at the difference in the replies that Bill Nye and YEC leader Ken Ham provided during their debate a few years ago when each was asked if there is anything that could get them to change their mind. Nye responded that evidence could whereas Ham intoned that nothing could.

Well, I'm willing to hear the evidence. Let the discussion continue!

Blessings,
Lee

[rogue06]

No, I want to know what's true, and I find your counterarguments have counters to them.

Blessings,
Lee

You continue to go back to the same sources that time and time again have been shown to have fed you misinformation either through ignorance or design. At what point will the old adage "fool me once shame on you, fool me twice shame on me" start to sink in? Or maybe Proverbs 26:11

[lee_merrill]

A minimum of 422 post date the split, plus the drosophila specific ones that are present in all genera.

422 new genes?! I could believe 422 mutations.

I only know of subnetworks in terms of ethernet. Maybe you can clarify that.

The authors referred to subnetworks, but you may call them networks if you prefer, so you are saying there is no reason to suppose that generation of networks would be more difficult?

You've not addressed the fact that we have actual worm tracks leading to actual worms in Ediacaran deposits. Ergo, bilaterians necessarily predate the Cambrian. What part of that don't you get?

Well, the worms that were brought up before Yilingia were debated, and are now debatable. But one creature in the terminal Ediacaran does not explain the complexity of the Cambrian explosion.

Blessings,
Lee

[lee_merrill]

You continue to go back to the same sources that time and time again have been shown to have fed you misinformation either through ignorance or design. At what point will the old adage "fool me once shame on you, fool me twice shame on me" start to sink in? Or maybe Proverbs 26:11

You're skipping my points! Please address my replies, or I shall begin to think your dedication to evidence is lacking...

So what is a rough probability of each step? .9 ^2000 is about 3 x 10^-92

Irreducible complexity? May I ask if you have read one of Behe's books? I've read The Beak of the Finch and Finding Darwin's God.

Blessings,
Lee

[rogue06]

You're skipping my points! Please address my replies, or I shall begin to think your dedication to evidence is lacking...

So what is a rough probability of each step? .9 ^2000 is about 3 x 10^-92

Irreducible complexity? May I ask if you have read one of Behe's books? I've read The Beak of the Finch and Finding Darwin's God.

Blessings,
Lee

You are having difficulties understanding probabilities and conflating unlikely with impossible.

Think of it this way. Take a deck of cards and shuffle them several times thoroughly. Now start laying them down face up one by one. The odds that they would lay down in that particular order are indeed astronomical -- but there you are looking right at it.

As for Behe's books... When Darwin's Black Box came out in the late 90s I was excited. I thought finally here was something that wasn't just a bunch of worn out PRATTs. I went out and bought a few copies and gave them to a couple of friends who tended to heavily rely on the aforementioned PRATTs. Imagine my disappointment after reading it. Essentially little more than a God-of-the-gaps argument wrapped in scientific lingo.

I've also read a good bit (probably about three quarters) of his The Edge of Evolution and was equally unimpressed

[shunyadragon]

You're skipping my points! Please address my replies, or I shall begin to think your dedication to evidence is lacking...

So what is a rough probability of each step? .9 ^2000 is about 3 x 10^-92

This use of probability is not based on scientific evidence in genetics, and is unethical and dishonest. and the simple answer is NO! No one is skipping your points. Your using unreliable non-scientific sources.

Irreducible complexity? May I ask if you have read one of Behe's books? I've read The Beak of the Finch and Finding Darwin's God.

Blessings,
Lee

Yes, it is a terrible book and not science. It is an attempt to justify ID without objective knowledge.

I have already trashed Behe's dishonest use of probability with references many times.

[TheLurch]

422 new genes?! I could believe 422 mutations.

This is obviously something you have difficulty with, but i'll say it again: reality is true whether you want to believe it or not. So many of our problems here come from the fact that what you want to believe isn't actually true, and you seem to be incapable of resolving that.

Here's the reality: evolving new genes really isn't that difficult. All new species seem to have at least a few new genes. This paper just shows how many a cluster of fast-breeding species can evolve.

The authors referred to subnetworks, but you may call them networks if you prefer, so you are saying there is no reason to suppose that generation of networks would be more difficult?

It depends. If you duplicate an entire pathway, as with nodal signaling, there's nothing new to evolve. If you link part of one pathway to part of a different one, then it's really not that difficult. Evolving every component of an entirely new pathway, even if you piece them together via domain swapping, is more involved and will accordingly take more time.

Since many of these things appear to be wholesale duplicates of existing pathways, then the cases i've looked at aren't very involved.

Well, the worms that were brought up before Yilingia were debated, and are now debatable.

Just because you listen to a bunch of hucksters that debate these things, doesn't mean they're actually debatable, any more than the arguments of the flat earth folks make the shape of the earth debatable.

Some of this evidence has been the subject of debate by actual scientists (mostly the embryos). But some of it really hasn't, and the new evidence is decisive. What does it say about you that you seem to be incapable of acknowledging it?

But one creature in the terminal Ediacaran does not explain the complexity of the Cambrian explosion.

No, it doesn't, but that's not what i'm using it to do. But it's a clear demonstration that the people who wrote the blog post don't know enough biology to know that talking about the Cambrian isn't relevant to a paper on the origin of bilaterians. That's the whole point of bringing this up: that the people you admire so much haven't got a clue. They start with a paper on one topic, and then dump a whole bunch of information that's completely irrelevant to the topic they started out on.

it's all there, plain as day. You've acknowledged pretty much all the pieces. So why can't you just acknowledge the obvious conclusion: the authors of the blog post made a fundamental error by starting out talking about the origin of bilaterians, and then spending the whole blog post discussing material that was irrelevant to their origin?

It's obviously true. Please acknowledge it.

[rogue06]

This is obviously something you have difficulty with, but i'll say it again: reality is true whether you want to believe it or not.

That reminds me of the quote by Lemony Snicket (pseudonym of Daniel Handler)

Just because you don't understand it doesn't mean it isn't so

Essentially, Argument from incredulity

[lee_merrill]

You are having difficulties understanding probabilities and conflating unlikely with impossible.

No, I'm not saying unlikely is impossible.

Think of it this way. Take a deck of cards and shuffle them several times thoroughly. Now start laying them down face up one by one. The odds that they would lay down in that particular order are indeed astronomical -- but there you are looking right at it.

You are making the same mistake TheLurch made in this thread, P(A|A) is indeed 1, but this is not the same as P(A), considering event A before the fact.

As for Behe's books... When Darwin's Black Box came out in the late 90s I was excited. I thought finally here was something that wasn't just a bunch of worn out PRATTs. I went out and bought a few copies and gave them to a couple of friends who tended to heavily rely on the aforementioned PRATTs. Imagine my disappointment after reading it. Essentially little more than a God-of-the-gaps argument wrapped in scientific lingo.

No, it's not a God-of-the-gaps argument, it's a probability argument. The more unselected steps evolution has to get through, the exponentially less likely the result is.

Blessings,
Lee

[TheLurch]

No, it's not a God-of-the-gaps argument, it's a probability argument. The more unselected steps evolution has to get through, the exponentially less likely the result is.

It's actually both god of the gaps and personal incredulity: I can't imagine how this can be selected for, therefore it couldn't have been, therefore god.

As an added bonus, Behe more or less adds "While we're at it, let's throw out some of the rules that are central to all of science, since they're turning out to be inconvenient to me."