The Cambrian Explosion

I'll enjoy seeing your mathematical analyses on the antievo fare. I've got Meyer's book slated for coverage in the revisions of #TIP on the Cambrian at www.tortucan.wordpress.com, of course, but until I can get around to that, I have dissected his chapter on Punctuated Equilbrium in the course of cataloguing pundits on that, see TIP 1.3. Upshot: Meyer never bothers to investigate any actual application of Punc Eek, and so didn't realize he didn't actually understand it, even to point of falsely claiming Gould & Eldredge invented allopatric speciation concept just to explain the supposed problems of the fossil record, when it was Ernst Mayr's 1930s concept that Gould/Eldredge then applied to the fossil context.

Two thoughts:

First, even if the Cambrian explosion were a deadly blow to evolution (which it isn't, but even if it were), where would that get us? There is a long way to go from "we don't know where all that diversity came from" to "therefore it was created by an intelligent agent", much less to "therefore it was created by the Christian god" or "therefore we are definitely not related to monkeys", which even if many IDers would deny it is what most of the readers of the book want to conclude.

Second, as a botanist I can only deplore the customary discrimination of plants on display in these cases. The sudden appearance and dominance of flowering plants is a mystery that already puzzled Darwin and has still not been solved to satisfaction; there are numerous fossil candidate lineages of 'seed ferns' etc. but it is controversial which of them, if any, are closest to the ancestors of flowering plants, and a few crucial snapshots are either missing or, more likely, sitting somewhere in museums without anybody recognising them for what they are because the crucial organs were too small and soft to be preserved.

But do the creationists write a book about about plants that I can read and laugh about? Noooo, always only those animals. It is really unfair.

Jason – good to see you back on the case, it would be a real shame if you gave up altogether, and I look forward to the magnum opus about mathematical anti-evolutionism. It seems that Meyer’s goose was cooked long before his 2013 offering on doubts about Darwin, but yet another nail in the already well secured coffin lid can’t do any harm.

One small point – I’m not sure that “at some point a critter is just too simple for it too fossilize”. Given that some very simple critters (simple enough to be micro-organisms) have left fossilised remains in stromatolites dated at approx. 3.5b years , it would seem that there is always some small chance that something might be preserved even in the most unlikely circumstances – if it just happened to die at the right time in the right place, where conditions just happened to be conducive to the fossilisation process. Gaps in the Cambrian or pre-Cambrian, increasing in size as we go back in time, are more likely the result of a) these conditions for fossilisation not being met very often, b) the very limited number of formations that survive from these times in the first place (as you point out), and c) the relatively short time span covered (despite it being, again as you point out, more than lengthy enough to override Meyer’s objections).

Well written professor.

A question that I don't know how to answer: what are the odds of a dead creature actually being fossilized? I realize that the odds are low, but how low?

sean s.

Rather than "Consider first that there are just a handful of places on Earth where rocks of Cambrian age exist." Perhaps it is better said that there are few places on earth where rocks of Cambrian age are accessible. Consider for example in the US most of the country is underlain by cambrian rocks, all be it they are covered by younger rocks (take the great plains for example). Or look at the Grand Canyon, and consider that the Tonto group at the grand canyon continues back away from its exposure at the canyon itself. Or in the UK that the Cambrian actually underlies all of england east of the type section area.

One thing that is quite clear is the genetic connection between all extant organisms. If we had all of the genomic data, we could trace the paths between them. For instance, the path from the common ancestor of hippos and cetaceans to modern cetaceans could be drawn - highlighting the changes within existing genes and gene families and the arrival of any novel genes. I just read that the Discovery Institute received $2.8M to deny climate science - I am sure that could get this amount to show in actual numbers the changes above instead of the bogus probabilities they are currently throwing out. If they are so devoted to science, why aren't they willing to any?

The book is mostly about The Cambrian Explosion.

Well, no, as it turns out. The Cambrian Explosion is just the hook to get you interested, and it takes up the first few chapters. But the meat (such as it is) of the book comes later, when he proves conclusively that a) we know nothing about evolution except that b) anything more than trivial amounts of it is impossible. And then he explains why: Behe said this, Dembski said that, Doug Ax said yadda yadda, and epigenetics too.

But the take-home message is that no matter how long you give evolution, no significant change can take place. So the whole thing about the fossil record, shortness of the Cambrian explosion, etc. is irrelevant. Evolution is just impossible. Period. No birds from theropods, no humans from apes, nothing at all more complicated than changing colors in Biston betularia.

Oh, and in the last chapter, God.

"Oh, and in the last chapter, God."

Why do people always give away the ending? "The butler did it with the sucker spear."
"The ex-wife did it with poison in the single malt."
"God did it with a flick of his pinky."

Spoils all the good mystery books.

Sean:

A question that I don’t know how to answer: what are the odds of a dead creature actually being fossilized? I realize that the odds are low, but how low?

Heh according to the kid's game "see if you can become a fossil" at the Smithsonian Museum of Natural History, it ranges from a top of about 30% for plant pollen down to hundredths of a percent for jellyfish. I expect those numbers assume the body isn't eaten/used by other plants and animals (because you do occasionally want the kiddies to win) so its an overestimation possibly by orders of magnitude.
But it was interesting from the perspective that - if you consider only a few factors and hold all the really complicated stuff constant - plant pollen fossilizes more easily than most other stuff.

If people want to see a theological response to Meyer's book and ID v. theistic evolution, they should look at Biologos' multi-prong review and Meyer's reply. They accuse Meyer of a "secular" approach - which is too funny.

Sean,

Like eric wrote, it depends. Particularly good chances are for organisms that are numerous, have tough skeletal parts, and live above or next to areas where their dead bodies can be covered quickly by the next layer of sediment. Diatoms are a good example.

One of the main points of the Cambrian explosion was that it was the time when hard exoskeletons really came into their own in diverse lineages; in other words, the Precambrian ancestors of those hard-bodied Cambrian organisms did not have the same hard exoskeletons and were thus vastly less likely to fossilise.

eric,

Pollen exines are actually really tough stuff. Palynologists use hydrofluoric acid, which dissolves glass and is highly poisonous, to remove all that annoying mud from the pollen samples they want to study.

"from about 541 million years ago to around 485 million years"
IDiots can't even understand that 541 - 485 = 56 million years really is a very long time and that hence it's nonsense to claim all kind of organisms suddenly came into existence.

"There is some debate among paleontologists about how long a period of time we’re talking about."
When I discussed this with a Dutch IDiot a few years ago I looked it up. The minimum seems to be 30 million years.

"Evolution is a slow process, but not that slow."
Any self-respecting IDiot is deaf, dumb and blind to this simple fact.

"So, forgive me, but what exactly is the problem here?"
Ask an IDiot and the answer will be, no matter how much you explain: Explosion. Evolution Falsified. The Tree of Evolution has fallen. That answer "applies" to your next questions as well.

"Why do I suspect that if I track down the articles from which these quotes came I would get a very different impression of what was being claimed?"
Golden Rule when having a discussion with an IDiot: he/she lies until proven otherwise. Thus far (more than five years now) this rule has never failed me.

Like some others I'm looking forward to your criticism of IDiot "math". It's something I'm not terribly familiar with and I'd like to refute nonsense such as "math proves 4,5 billion of years is not enough for evolution from dust to man."

@2 ASL complains: "But do the creationists write a book about about plants that I can read and laugh about? Noooo, always only those animals. It is really unfair."
What do you think of physicists then? Especially those who are interested in superconductivity at relatively high temperatures? Science can't explain it! And it's not that they didn't try; after all there is probably (compare BCS theory) a Nobel Price waiting.
But they can't, just like you can't explain flowers. Must be god - oops, an Intelligent Designer, blessed be Him/Her/It - juggling with magnets. But do you ever, ever hear an IDiot talking about that? Ha. So you should rather have pity with the poor physicists!

“It looks like the animals just appeared out of nowhere!”

That’s not something said by Creationists alone.
Charles Darwin was worried about the Cambrian Explosion (CE), and over a hundred years later Harvard’s Stephen Jay Gould was worried enough about the CE that he invented a whole new (but now largely abandoned) theory, Punctuated Equilibrium. And more recently, Richard Dawkins said "It is as though they [CE fossils] were just planted there, without any evolutionary history."
........

“There is some debate among paleontologists about how long a period of time we’re talking about, but there’s no question that it is best measured in tens of millions of years.”

NO question? Really?
Perhaps you would do better to rephrase more like this: “There’s no question among paleontologists who have assumed the gift of INFALLIBILITY regarding the accuracy of radiometric dating assumptions, and the radiometric dating which, for some reason, has never been applied to allegedly 75-million year-old dinosaur bones which contain unexplained unfossilized soft tissue. But there ARE questions among others.”

I think that would be a truer, more accurate statement. Don’t you?

...............
“Which part of this is supposed to make me think that evolution, which proves its worth in thousands of books and papers each year…”

Jason, would you PLEASE provide here JUST ONE such paper? Just ONE paper (internet accessible, please, so that we all can read it).
I have never seen such a paper, so, I’d like to see what you’re talking about.

....
“The little data we have about the Cambrian and Precambrian is entirely consistent with evolutionary expectations…”

Really? I thought I remembered reading about lots of surprises in the Cambrian. I did a little digging tonight and found this, for example. It’s titled “Cambrian fossil pushes back evolution of complex brains”. Some excerpts, with[my notes]:

"No one expected such an advanced brain would have evolved so early in the history of multicellular animals," said Strausfeld, a Regents Professor in the UA department of neuroscience.”
[Sounds not entirely consistent with evolutionary expectations, don’t you think?]

“According to Strausfeld, paleontologists and evolutionary biologists have yet to agree on exactly how arthropods evolved, especially on what the common ancestor looked like that gave rise to insects.”
[Hmmm.]

“… They argue the fossil supports the hypothesis that branchiopod brains evolved from a previously complex to a more simple architecture instead of the other way around.”
[Whoa! Did you catch that? A simpler brain evolving from a more complex brain. That’s surprising, I would think.]

"It is remarkable how constant the ground pattern of the nervous system has remained for probably more than 550 million years," Strausfeld added. "The basic organization of the computational circuitry that deals, say, with smelling, appears to be the same as the one that deals with vision, or mechanical sensation."
[So, brains evolved very quickly, and very quickly got more complex (or perhaps in some cases simpler (see above)), but have been essentially unchanged for the last 550 million years. That’s pretty unexpected, I would think. Don’t you?]

http://www.sciencedaily.com/releases/2012/10/121010131436.htm

How did the more complex body types of the Cambrian come to be?
And why would they come to be?

Complexity gets pretty complex pretty quickly.

From http://www.cell.com/current-biology/abstract/S0960-9822%2813%2900915-9
“The establishment of a multicellular body plan REQUIRES COORDINATING changes in cell adhesion and the cytoskeleton to ensure proper cell shape and position within a tissue. Cell adhesion to the extracellular matrix (ECM) via integrins plays diverse, essential roles during animal embryogenesis and therefore MUST BE PRECISELY REGULATED [ 1 ]. Talin, a FERM-domain containing protein, forms a direct link between integrin adhesion receptors and the actin cytoskeleton and is an important REGULATOR OF integrin FUNCTION [ 2 ]. Similar to other FERM proteins, talin makes an intramolecular interaction that could autoinhibit its activity [ 3–6 ]. However, the functional consequence of such an interaction has not been previously explored in vivo. Here, we demonstrate that targeted DISRUPTION of talin autoinhibition gives rise to morphogenetic DEFECTS during fly development and specifically that dorsal closure (DC), a process that resembles wound healing, is delayed. Impairment of autoinhibition leads to reduced talin turnover at and increased talin and integrin recruitment to sites of integrin-ECM attachment. Finally, we present evidence that talin autoinhibition is regulated by Rap1-dependent signaling. Based on our data, we propose that talin autoinhibition provides a SWITCH FOR MODULATING adhesion turnover and adhesion stability that is ESSENTIAL FOR MORPHOGENESIS.”

Whoa!

Shorter See Noevo: Every time some new insight about natural history is gained, evolution is proved wrong and goddidit, because biologists did not precisely predict every detail of the new discovery.

For sn it's mote like "I can't understand the papers and I'm too lazy tontry, so I'll just pollute the discussion with a bunch of
lies."

This blog is generally excellent, and over the years has provided some first rate discussions with many useful contributions from numerous sources.
Sadly, it seems that there is now some threat to this fine tradition. Jason’s commitment to allow free expression in so far as this is reasonable is admirable, and he should certainly be supported in this by his contributors. However, it also behoves those contributors to be equally reasonable in return, and in this respect there does now seem to be a problem.
Nobody can object to contrary views being freely and honestly expressed, but in recent months we have witnessed the blog being assaulted – one might say trolled – by a few contributors. They know who they are, but the most egregious culprit (at least over recent posts) is undoubtedly the individual who styles himself “See Noevo” (which he surely doesn’t, and won’t). This latest post, which should surely give a good opportunity to discuss the “Cambrian Explosion”, is now under the threat that it might go down the same route as several other recent discussions, and also get itself side-tracked down See Noevo’s blind alley. Can we please prevent this?
I would venture to suggest that nobody bother to point out his errors, just leave him alone. I can’t recall whose quote this is, but someone once pointed out that “arguing with creationists is like arguing with squid”. By now it must surely be abundantly clear to all of us that he will not listen, he is incapable of any critical thinking with regard to possible modification of his own views, and he will never give a satisfactory response when his errors are pointed out to him.
Can I please implore dean, Michael Fugate, Alex SL and others to desist from encouraging this truculence? You really are just battering your heads against a brick wall, which ends up being greatly detrimental to the blog as a whole. Given Jason’s generally open generosity in putting up with a great deal of aggravation in the name of free speech, can we not agree to help him out by refusing to take long trips down blind alleys? The See Noevos of this world are never going to desist on their own, and have clearly immunised themselves very effectively in a bubble of protection resistant to any sort of rational discourse.
Stop feeding the dog!

MNb says

“Why do I suspect that if I track down the articles from which these quotes came I would get a very different impression of what was being claimed?”
Golden Rule when having a discussion with an IDiot: he/she lies until proven otherwise.

See Noevo says:

Charles Darwin was worried about the Cambrian Explosion (CE), and over a hundred years later Harvard’s Stephen Jay Gould was worried enough about the CE that he invented a whole new (but now largely abandoned) theory, Punctuated Equilibrium. And more recently, Richard Dawkins said “It is as though they [CE fossils] were just planted there, without any evolutionary history.”

So we have an hypothesis put forward by MnB and a test case offered by See Noevo. Let's plug the quote into Google and see what we get....
Well lookie here, that exact quote shows up as the quote mine project's #40. Seems its such a common misquote by creationists it made the list. Reading the full quote and explanation shows that Dawkins was not "worried" about the Cambrian explosion. He's fine with the standard explanation (that the soft-bodied organisms preceding the Cambrian didn't fossilize well). So was Gould. See Noevo is taking the sentence out of context, taking a quote meant to skewer punctuated equilibrium and trying to pretend Dawkins was saying something about the ToE writ large. In truth, Dawkins was saying the CE is not evidence for punctuated equilibrium because on such time scales and for the specific case of soft-bodied critters evolving into bony critters, punc-e and gradualism look the same. The CE is consistent with both, it doesn't favor one over the other.

Phil B, I had the same thought, which is why I deliberately refrained from replying as such but merely provided a TLDR; summary of his argument.

Wasn't it pigeons instead of squid?

Unfortunately I don't have a lot more to add on the post except that I enjoyed Among the Creationists very much and am looking forward to the book the host of this blog is planning.

You really are just battering your heads against a brick wall, which ends up being greatly detrimental to the blog as a whole.

I disagree. When I reply to someone like See Noevo and try to explain science or demonstrate an error, I'm not just doing it (just) to try and convince him, but to give accurate info to any lurkers who might otherwise be swayed by his bad arguments. His Dawkins out of context quote is a great example. Without the right context, that quote sounds pretty damning of evolution. And this is Dawkins! If he doubts evolution can explain the CE, certainly we should too, right? That's the message See is trying to communicate. But Dawkins isn't saying evolution can't explain the CE. He thinks the ToE explains it perfectly well. He disagrees with the notion that punc-e explains it better than gradualism, and that is what that quote is about. Explaining this context to lurkers (regardless of whether See Noevo will learn anything from it) is, IMO, useful.

What we are learning about the Cambrian Explosion shows the wonder of science. We make assumptions about what can and cannot happen out of convenience. When evidence challenges these assumptions, we reconsider them - and if the evidence is strong enough, we change them to match the evidence. For SN's ilk, this is a weakness.

The examples @14 & 15 show that some assumptions need to be reconsidered. Perhaps soft tissue can last millions of years under the right conditions - to state definitively that it cannot would be difficult to prove (besides, if dinosaur bones were so young, wouldn't we find soft tissue more frequently?). The Cambrian Explosion offers a richness of opportunity for expanding our knowledge of evolution, and if we find a rabbit, to challenge it.

I suppose it's time for everyone who wants to talk about the supposed "sudden appearance" of the Cambrian fauna to google "small shelly fauna", a term that nobody has mentioned so far but should. The SSF begins in the latest Precambrian and gradually increases in diversity and complexity until the record of the "explosion" proper starts with the first trilobites and the Chengjiang fossils. Call it 25-30 million years. Add in the ichnofossils (burrows and trails), which do something similar, and you can see that this "sudden appearance" is a matter of taphonomic conditions (the technical term for what results in preservation) and ignorance or suppression of the published data.

Meyer mentions it in a footnote but otherwise ignores it, as the SSF is inconvenient to his claims. A good corrective to Meyer is reading a real book about the Cambrian. I recommend D. H. Erwin & J. M. Valentine. 2013. The Cambrian Explosion: The Reconstruction of Animal Biodiversity. Roberts & Co, Greenwood Village, CO.

Alex SL – I take the point. As for pigeons and squid, I think they are 2 separate quotes, but both equally apposite in this context. I share your sentiments on the 2 books, one I also enjoyed, the other to come.

eric - I do understand your desire to appeal to the “lurkers”, as you so generously refer to those who are yet to be educated on the evo/creationism argument. I think this goes to the heart of the evo/creationist argument as a whole. I agree that whilst we cannot hope to convince the already hopelessly deluded (e.g. See Noevo), we should certainly be striving to make sure that those yet to discover and enter this controversy should be well appraised of the facts in the first place. In this respect I can only praise your efforts, and those of others like-minded. However, this still leaves a problem – how are we supposed to have a well informed and meaningful discussion over aspects of evolutionary theory, if we constantly have to submit to interference from the See Noevos of this world who will inevitably drive us back into this ludicrous controversy every time we try to engage publicly? Surely there must come a time when we must leave the PRATTs alone, rather than just add another few dozen refutations to the thousands already out there, at the expense of yet again sacrificing the whole discussion on the altar of these deluded fundies. Help me – where’s the way out?
I would be interested in Jason’s view on this – when the blog raises aspects of evolutionary science (as it so often does), to what extent does he consider his blog’s purpose to be that of promoting a sensible scientific discussion or, alternatively, to what extent does he consider the purpose to be for refuting creationist garbage to a scientifically uneducated audience who need accurate information and answers to creationist claptrap?

Seems like something of a dichotomy to me.

To Walt Jones #22:

“…the wonder of science. We make assumptions about what can and cannot happen out of convenience. When evidence challenges these assumptions, we reconsider them – and if the evidence is strong enough, we change them to match the evidence. For SN’s ilk, this is a weakness.”

No.
For those of my ilk, this is a weakness for EVOLUTION “science” in particular, not for real science. What you describe is a strength for legitimate science, and indeed, for any field of inquiry. However, what I’ve found over and over in reading the evo science literature is that no matter what is discovered, the essential epiphany (i.e. evolution happened) NEVER changes.
……

“…besides, if dinosaur bones were so young, wouldn’t we find soft tissue more frequently?”

They ARE finding dinosaur soft tissue more frequently. You can find many different examples with a little Googling.
Here’s an article published this week:
http://www.nature.com/ncomms/2015/150609/ncomms8352/full/ncomms8352.html

Some excerpts:
“Exceptionally preserved organic remains are known THROUGHOUT the vertebrate fossil record… and their preservation is MORE COMMON than previously thought.”

“… putative soft tissue (either erythrocyte-like structures, collagen-like, fibrous structures or amorphous carbon-rich structures …) was observed in SIX OF OUR EIGHT dinosaur specimens… and this strongly suggests that the preservation of soft tissues and even proteins is a more COMMON PHENOMENON than previously accepted.”
……………

“ The Cambrian Explosion offers a richness of opportunity for expanding our knowledge of evolution, and if we find a rabbit, to challenge it.”

Boy, talk about tropes.
As I said to eric on another thread here recently, I am highly confident that if such a wascally wabbit was ever found, evolution theory would still reign from the throne. Darwin’s queen would just be modified a bit. New duds, a new doo. Whatever. Whatever it takes to keep her on her seat. And sit she will.
I can just imagine it in now: “What a surprise! Scientists have discovered the fossil of a rabbit in the Cambrian. HOWEVER, SOME scientists are NOT in complete agreement that it was a rabbit, or that it was Cambrian. This will, OR COULD, drastically change our understanding of….. [page down],

… how….[page down again, past the advertisement]

…. EVOLUTION HAPPENED.”

Oh dear, here we go again. Please everyonre, ignore.

If one truly wanted to understand how complexity arose - simply search for "homeobox" in your favorite search engine. Found throughout multicellular organisms (plants too!), their duplication easily leads to more complexity through segment repetition and subsequent diversification.

To add on to that -
homeostasis is key and feedback loops develop throughout the universe not just in biological systems - see "Earth Systems"
once you have one gene simply duplicate - that one gene works so minor tweaks can give it a new function and major ones won't kill the organism;it already has functionality.
once you have one cell simply duplicate
once you have one segment simply duplicate
You will note that biologist thought that humans would have many more genes than they have - the difference between a worm at the beginning of the Cambrian and a human is minor.

To Phil B #24:

You directly call me “hopelessly deluded” and indirectly a “PRATT”. [I had to look up the meaning of the latter.]

I’ll grant you I’m no Einstein. However, I do think I have and exercise some common sense, reading comprehension and critical thinking. [And shockingly, I even have some education, including a masters from the Ivy League. Sadly, the diploma was not in any of the “evolutionary” sciences.]

I’ll also grant you that in my life I HAVE been “deluded”, although not hopelessly. My life is a demonstration of how no one is necessarily “hopelessly” anything. See, I was deluded for about 30 years, during which I believed in evolution. But then, around my mid-forties, I started reading the evolution science community’s own literature. That was over 12 years ago. Long story short, hope DOES spring eternal, and I’m no longer deluded. I’ve “evolved” on evolution. I think it may be one of the worst forms of “junk science.”

And as a scientist in spirit, I will speak up for the truth and will question what bears questioning.
At least, I’ll do so as long as I can, before debate is shut down.
Before someone actually ENFORCES “the debate is over”.
I guess it’s only a matter of time.

P.S.
On a related junk science topic, signs of shutting down the debate are there for all to see: https://www.youtube.com/watch?v=64n8WZdk-qQ

Phil B’s comments at #24 are correct.

SN’s complaint at #29 also has some merit, but very, very little. I’ve commented to SN enough to know that there’s no set of facts that would ever bring SN to question his position vis-à-vis evolution. The fact that there is so much in biology that confirms evolution yet SN is not aware of any of this is proof enough that SN’s playing a different game. There’s nothing to be gained, so I’ve sworn of that vice.

sean s.

Why would biologists give up on evolution? Surprises are expected, evolution works, and there’s no scientific alternative. Giving up on it would be irrational. Without evolution, nothing makes sense in biology. Without evolution, biology is reduced to a collection of unrelatable facts.

sean s.

It's worth pointing out that sn is rather a universal science denier. He has expressed much of the same level of ignorance and disbelief about modern cosmology as he has about evolution, for example, and for much the same reason: he refuses to read the articles to which he's been referred. The phrase "lost cause" is probably a gross understatement for a description of him.

this still leaves a problem – how are we supposed to have a well informed and meaningful discussion over aspects of evolutionary theory, if we constantly have to submit to interference from the See Noevos of this world who will inevitably drive us back into this ludicrous controversy every time we try to engage publicly

Commenting is free and essentially infinite in the amount you can do. if you want to have a conversation with someone here about in-depth matters of science, go for it. My responding to See Noevo doesn't prevent you from doing that. And in fact sometimes the same people do both at the same time.

As any one familiar with pedagogy would know, the difference between experts and the rest is practice. Practicing one's craft makes one an expert. This is why creationists are experts at apologetics and not science. This is why SN, even though claiming to have once accepted evolution, can claim that he no longer does - he was never an expert in any science and especially biology. He does excel at apologetics, though.

Then consider that at some point a critter is just too simple for it too fossilize, and it becomes inevitable that you are going to find some jumps in complexity.

Not necessarily. Ways around this:
1) Structurally simple creature leaves an identifiable chemical trace. (key word: biomarkers)
Unravelling ancient microbial history with community proteogenomics and lipid geochemistry, Brochs and Banfield, doi:10.1038/nrmicro2167

2) Structurally simple creature bands together with zillions of others to form a macroscopic structure. (key word: stromatolite)
Cyanobacteria: Fossil Record

John Harshman #23: I suppose it’s time for everyone who wants to talk about the supposed “sudden appearance” of the Cambrian fauna to google “small shelly fauna”

i second the motion. If you prefer a simpler presentation than Erwin & Valentine, I can recommend Evolution: What the Fossils Say and Why It Matters by Donald R. Prothero, ISBN: 9780231139625
It should be accessible to anyone with an 8th grade education.

See@25
I disagree and stand by my comment.

SN:

I think it may be one of the worst forms of “junk science.”

Okay, describe a scientific, testable hypothesis for the origin of new species that is better.

Let's say I'm a proposal reviewer. I have two proposals in front of me and can only fund one. Proposal 1 says they want to look for a fossil that has characteristics of both birds and oviraptor dinosaurs. They propose to look in rock radioisotopically dated to 160-200 Mya. Proposal 2 says they want to look for a fossil of 4-legged insects. They propose to look in rock 10,00-5,000 years old. Which proposal do you think has the better chance of turning up what they're looking for? What scientific theory do you have that would give me any reason to believe Proposal 2 had even a snowball's chance in hell of being successful? You want things like #2 funded, you have to come up with an hypothesis to support that decision. No hypothesis, no money. No money, no research.

It should be accessible to anyone with an 8th grade education.

and a willingness to learn.

If the creationists here really were as intelligent as they claim and really wanted to make a difference, they would go back and get retrained in biology, geology or astronomy and set out to test their hypotheses (if they have any) in a rigorous manner. This is what people who are serious do. You become a scientist and engage in the science. Some creationists have of course gone through the motions getting a science PhD, but then go to work in apologetics. They aren't scientists.

Another author to consider is Sean B. Carroll and his books on EvoDevo.

eric at #33 –

You are clearly correct that it must be possible, at least in principle, to continue a “conversation with someone here about in-depth matters of science”, irrespective of See Noevo’s interjections and the responses of others thereto. I would even grant that, at least to some extent, you actually succeed in achieving this. Unfortunately this does not detract from the fact that SN and his ilk nevertheless manage (at times very effectively) to hijack the whole discussion and take it off in some direction which ends up greatly detracting from whatever the interesting points at issue may happen to be.

I hope you will concede that I have not at any point wished to deprive the SN clique of their freedom of expression. Far be it from me to restrict anyone else’s free speech. My point was simply that in engaging with such individuals at such length, we end up allowing the whole exchange to be seriously devalued. We do not deny SN and co. any of their basic rights by electing to ignore them – though I concede that the occasional put down may be useful, surely we don’t need to spend huge numbers of column inches refuting every point – the very PRATTS that SN now seems to be accusing me of counting him, as a human being, of being among! (work that out!). Had he actually googled just exactly what a PRATT is, he would have realised that it is not in fact a person (deluded or otherwise).

Phil B.

I'll own this: I googled "PRATT" and I cannot figure out what you mean by it.

sean s.

point refuted a thousand times

To sean samis #31:

“Giving up on [evolution] would be irrational. Without evolution, nothing makes sense in biology. Without evolution, biology is reduced to a collection of unrelatable facts.”

Your paraphrase of Dobzhansky is one of the most deranged declarations from Darwinists.
There is not one, single advancement in biology for which a belief in evolution was required. This very subject was discussed at some length over at http://scienceblogs.com/insolence/2015/05/20/why-do-doctors-deny-evolut…

… where I started the discussion with this comment:
“Obviously, one can be a world-renowned medical doctor without believing in evolution (e.g. Ben Carson).
But I have two questions right now:
1) Does the med school curriculum include at least one course on biological evolution?
2) Can anyone name just one medical breakthrough or current medical treatment or procedure which required a belief in evolution?”

That was comment #21. Now, we’re at well over 1,400 comments (on this and other topics).

Ah. that did not show up on my google search. Lots of stuff about a Certain Canadian Poet, and P&W, but...

sean s.

You are boring us SN, yawn.....

I googled "evolution and medicine" and found some very quickly. SN's not even trying.

sean s.

Anyone in biomedical research who claims evolution doesn't undergird his or her work is a prat with one t. Common ancestry underlies all animal research - without it all those experiments would be a waste of time, talent and money and just cruel abuse of animals for no reason.

Just today in Nature there is an article discussing population structure of Bronze Age Europe and that along with studies of those who died and those who survived the Black Death can give us insight into evolved resistance to disease.

Sean at #41 - just to shore up Michael's note at #42 :-

http://rationalwiki.org/wiki/Point_refuted_a_thousand_times

I am glad to see the word expert being used here instead of authority. The dates in the rocks don't line up because some paleontologist ordered them to. Rather, there are patterns of phenomena in nature, and some people, through hard work and lengthy study, understand it better than others.

To eric #38:

“Let’s say I’m a proposal reviewer. I have two proposals in front of me and can only fund one. Proposal 1 says they want to look for a fossil that has characteristics of both birds and oviraptor dinosaurs. They propose to look in rock radioisotopically dated to 160-200 Mya. Proposal 2 says they want to look for a fossil of 4-legged insects. They propose to look in rock 10,00-5,000 years old. Which proposal do you think has the better chance of turning up what they’re looking for?”

First, I’d ask each WHY he/she/it is looking for what he/she/it is looking for.

Second, after listening to he/she/it for a while, with his/her/its attempted justification being something about evolution, I’d say:
“Excuse me, please. Something actually important and urgent has come up. I’ll have to ask you to leave. Or perhaps you’d like to sit outside in the waiting room. My secretary can provide you with some magazines she finds entertaining, including People Magazine, Cosmopolitan, and The Journal of Evolutionary Biology.”
[Regarding my “important and urgent”, see related points in comment #43.]

Third, I’d bring in the guy with a THIRD proposal, this one for a possible TV series called “The Fossil Whisperer”. The fossils won’t speak about boring stuff like exactly what they are and when they lived and what they were transitional to, but rather with more popular stuff. For instance, the old wise fossils will give the Whisperer/Listener advice on “reproduction”, if you know what I mean [wink, wink].
It may be R-rated. But whatever the details about the fossils’ wisdom on reproduction or whatever, it’ll sort of tie into evolution as an afterthought at the end. You know, to give some kind of appearance of legitimacy or believability to moderns. Other episodes of “The Fossil Whisperer” might cover mutations, or specifically, the popular fictional mutants we call “zombies”.

Fourth, I’ll schedule a second meeting with this gentleman because I’m liking what I’m hearing. I think this could be a winner. This could REALLY sell. THIS is entertainment the moderns may like.

Fifth, I’d reschedule a meeting with a gal who has a FOURTH proposal, something about some new science or technology that could actually impact our lives, and impact them positively. I’d tell my secretary to reschedule for a time as soon as possible, hopefully for tomorrow, because it sounds important and urgent, and I’m very interested. Because I’m very interested in spending my research money wisely.

Sixth, I’d tell my secretary to cancel any future meetings on those first two proposals.

Seventh, I’d then take a rest, like on the seventh day, by heading out to the golf course.

Now come on guys - is anyone really going to dignify #50 with any sort of point by point response?

Thanks, Phil B. When I read Michael’s note, I reread your first use of the acronym and it fit perfectly, so I was convinced.

Dunno why Google didn’t locate the rationalwiki.org entry, but c’est la vie.

sean s.

One can read bits and pieces of Meyer's book at Amazon. The last couple of chapters are straight up apologetics - complete with the child schooling the elders (Jesus in the Temple anyone?) and personal statements of faith. Barf.

For instance, he claims scientists have fettered themselves to naturalism and by fiat exclude intelligent design. But wait, couldn't the intelligence be natural? Weren't we told ID didn't know who the intelligence was? Why does it need to be supernatural?

Also he is claiming that design can't occur without intelligence (by fiat no less), but this is nonsense - even if you exclude natural selection. There is plenty of design that occurs with any intelligence whatsoever. The book is buffoonery on a grand scale.

@46 (and @43): I think Shubin has a decent intro discussion of this near the back of Your Inner Fish. IIRC the upshot was that human neurological wiring makes little to no functional sense. A budding creationist neurosurgeon or medical student just has to brute-force memorize the way everything connects, because there is no rational design to it. In an evolutionary framework, it makes complete sense and is much easier to memorize: the fish-wiring evolved first and then additional neurological wiring got added on in a successive, evolutionary manner (land vertebrate stuff next, then mammalian stuff, then...). Yet another instance of, "if we are the product of special creation, then God sure went to a lot of trouble to make it look like we evolved."

Bayesian Bouffant;

“there are patterns of phenomena in nature, and some people, through hard work and lengthy study, understand it better than others.”

In deed true. Those who wish to understand must not try to force the phenomena to fit a preconception, but let it speak to them. Otherwise all the hard work and study will be for naught.

sean s.

@51: he didn't respond substantively to either of my questions. Didn't say what his alternative scientific hypothesis is, and didn't say how I should make this decision. He gave good advice on how to get fired from a proposal-evaluation job, though. So to answer *your* question....not me.

eric #56

"@51: he didn’t respond substantively to either of my questions."

When has he ever done?

@53:

For instance, he claims scientists have fettered themselves to naturalism and by fiat exclude intelligent design.

Behe, Dembski and Meyer have no such fetters. And at least the first two get research funding, and have for the last 20+ years. I have yet to hear of any single useful or even interesting discovery to be put out by this unfettered science. In fact if I was a prospective bio grad student and was told "work for Behe, and you'll publish as much novel and groundbreaking research as he does. Work for Lenski, and you'll publish as much novel and groundbreaking research as he does," it wouldn't be a hard choice. For all the talk about the wonders this unfettered research will bring, the actual unfettered researchers don't seem to be producing much. The output of unfettered research appears to be about one popular non-peer-reviewed book per decade per researcher or so, I'd estimate.

Regarding @53:

For instance, he claims scientists have fettered themselves to naturalism and by fiat exclude intelligent design./blockquote>

This is almost right, which makes it a sneaky lie probably.

Scientists have fettered themselves to empiricism and reason, which pretty much limits their reach to Nature. ID is excluded, by necessity: it is not subject to empirical analysis or reason, at least not yet. Likewise the supernatural.

All disciplines have fetters; that goes with the territory.

sean s.

Ack! bad HTML. My error.

Regarding @53:

For instance, he claims scientists have fettered themselves to naturalism and by fiat exclude intelligent design.

This is almost right, which makes it a sneaky lie probably.

Scientists have fettered themselves to empiricism and reason, which pretty much limits their reach to Nature. ID is excluded, by necessity: it is not subject to empirical analysis or reason, at least not yet. Likewise the supernatural.

All disciplines have fetters; that goes with the territory.

sean s.

To Phil B #40:

“We do not deny SN and co. any of their basic rights by electing to ignore them – though I concede that the occasional put down may be useful, surely we don’t need to spend huge numbers of column inches refuting every point – the very PRATTS that SN now seems to be accusing me of counting him, as a human being, of being among! (work that out!).”

I guess that’s clear enough. To some people.

“Had he actually googled just exactly what a PRATT is, he would have realised that it is not in fact a person (deluded or otherwise).”

Oh, I see now. My mistake. I guess I failed to pay enough attention to the CAPS.
http://www.urbandictionary.com/define.php?term=pratt

But certainly your characterizations of me such as “egregious culprit”, “squid”, “hopelessly deluded”, ‘hijacker’ still stand, yes?

But of course.

I’d bet you even have a sophisticated British accent.
I can hear it now: “The name’s B, Phil B.”

Which reminds me of one of the funnier scenes ever:
https://www.youtube.com/watch?v=OkChbEu3hKE

OK, I'll go as far as trading the occasional epithet with you, and I'm pleased you have realised that I did not call you a PRATT (or a "pratt", as in your urban definition).

Yes - I am British, with a British accent (sophisticated or otherwise, not for me to say), but the Bond comparison is overly generous, and flatters me to a degree I'm sure I don't deserve.

Wow. My estimation of SN is in freefall.

sean s.

To Phil B #62:

I’m sure, too.

It is not that intelligent design is impossible or even improbable; humans design things all the time - even other primates and birds. I mentioned a study last week where fish design a plan to hunt other fish. The problem is the analogy doesn't work with the design of living things - they aren't designed in the same manner that humans design. Natural selection, for all Meyer's extended whine, works just fine to design organisms. Meyer also sneers about theistic evolution - if one thinks natural selection is sufficient then what does a God do? Meyer doesn't exactly tell us what a God does either.

Regarding

Meyer also sneers about theistic evolution – if one thinks natural selection is sufficient then what does a God do?

Many years ago (in the previous millennia) when I was still a Christian, I would have qualified as a “theistic evolutionist”. That such a position is unacceptable to creationists is further indication that their complaint is religious; a religious complaint with science, scientists, and heretical Christians who are untroubled by evolution (as I was).

sean s.

<

>Meyer also sneers about theistic evolution – if one thinks natural selection is sufficient then what does a God do? Meyer doesn’t exactly tell us<

>

But that's always the case isn't it? Lots of complaining about how evolution can't be true because, well, because they just don't believe it, and so it's down to their (always theirs, never the possibility it could be someone else's) god - without any details there either .

May I suggest that everybody put See Noevo on killfile, which is available for both CHROME and FIREFOX. No need to bother win responding to his nonsense.

Colnago80,

Thanks, but SN’s not worth even that effort. Helps to have kids; you learn to ignore stuff quite easily.

sean s.

See, you’re being dishonest by quote-mining Dawkins work

In context, the full Dawkins text you've lifted your quote from reads

It is as though they were just planted there, without any evolutionary history. Needless to say this appearance of sudden planting has delighted creationists. Evolutionists of all stripes believe, however, that this really does represent a very large gap in the fossil record, a gap that is simply due to the fact that, for some reason, very few fossils have lasted from periods before about 600 million years ago. One good reason might be that many of these animals had only soft parts to their bodies: no shells or bones to fossilize. If you are a creationist you may think that this is special pleading. My point here is that, when we are talking about gaps of this magnitude, there is no difference whatever in the interpretations of 'punctuationists' and 'gradualists'.

To Michael Fugate #65:

“It is not that intelligent design is impossible or even improbable; humans design things all the time… The problem is the analogy doesn’t work with the design of living things – they aren’t designed in the same manner that humans design. Natural selection… works just fine to design organisms.”

How did natural selection design the first organism?

Do you happen to know of any definitive literature on how abiogenesis was designed?
Please link an article or two on it.
[From what I remember, abiogenesis has never been observed in nature nor coerced in a lab. But maybe you know something I don’t about natural selection’s design for abiogenesis.]

Thanks.

P.S.
In case you need more time for the abiogenesis demonstration, in the mean time I MIGHT settle for definitive literature on exactly how natural selection designed later organisms, or even later organs.

However, what I’ve found over and over in reading the evo science literature is that no matter what is discovered, the essential epiphany (i.e. evolution happened) NEVER changes.

And that essential 'epiphany' won't change, until sufficient new evidence accumulates to falsify evolutionary models. That hasn't happened, and in truth--given the extremely large body of evidence from multiple fields of scientific inquiry supporting an evolutionary origin for the biological diversity we observe-- is unlikely to happen.

In any event, should evolution ever be falsified it will be replaced by a different and entirely natural phenomenologic model for the origin of biologically diverse species--it won't be replaced by special creation.

The opposite of "Evolution did it", after all, is "Evolution didn't do it"--it isn't "God did it".

Thanks, but SN’s not worth even that effort.

It's rather like having a cat in the house. Most of the time there is no real benefit, but occasionally there is something that causes you to burst out laughing.

See @ 43

Yes See, the subject did come up over at RI--and when you were offered examples of advancements in biology which evolutionary derived from an understanding of evolutionary processes you simply ignored them.

RE: See @ 43 again,. the example I gave was identifying and understanding the etiology of cystic fibrosis, phenylketonuria, galactosemia, retinoblastoma, sickle-cell anemia, thalassemia, Tay-Sachs disease, Werner’s Syndrome, and other recessive autosomal disorders.

There’s your problem right there, See: living organisms, abiogenesis, organs, etc, are not products of directed and goal oriented design.

If you're going to attempt to discuss evolution intelligently, it would really be to your benefit to make some effort to understand what evolutionary models do and do not state and predict.

To JGC #72:

“In any event, should evolution ever be falsified it will be replaced by a different and entirely natural phenomenologic model for the origin of biologically diverse species–it won’t be replaced by special creation. The opposite of “Evolution did it”, after all, is “Evolution didn’t do it”–it isn’t “God did it”.

Would it be fair to say that, in YOUR eyes, should evolution ever be falsified it will be replaced or SHOULD BE replaced with some natural something, AS LONG AS that something is ANYTHING BESIDES “God did it”?

Would that be fair to say?

“Yes See, the subject did come up over at RI.”

What is RI?

that doesn't characterize my position at all. Even if there isn't anything else it would be wrong to embrace "God did it" to account for observed biological diversity, as 1) there is no evidence demonstrating that supernatural entities commonly termed "god' or "the gods" exist, and 2) "God did it" explains nothing--all it does it let you avoid the hard work of deriving a a productive and meaningful explanation by writing whatever isn't understood off to magic.

If you're going to embrace a supernatural explanation for the origin of living populations, any speculative supernatural entity of one's choice serves the purpose equally well--"god did it" is substantively and functionally indistinguishable from "Pixies did it", "Leprechauns did it", "Unicorns did it", etc.

RI is the blog where you've been failing to offer any meaningful arguments regarding evolution for the past several days, See.

Trial and error is a tried and true method to design even by humans - that is natural selection in a nutshell.

To JGC #75:

“RE: See @ 43 again,. the example I gave was identifying and understanding the etiology of cystic fibrosis, phenylketonuria, galactosemia, retinoblastoma, sickle-cell anemia, thalassemia, Tay-Sachs disease, Werner’s Syndrome, and other recessive autosomal disorders.”

JGC, why limit yourself to epidemiology or pathology?
There really is no end to what evolution explains.
But sticking with medicine, you could talk about, for example, orthopedics. You already have the video. All you have to do is maybe add the following after each line: “and the etiology of THAT bone is “It evolved!””
https://www.youtube.com/watch?v=e54m6XOpRgU

I look forward to the evolutionary update of that video.

The ignorance at 77 and 78 meets the cat analogy - it's where you point, laugh, and say "I can't believe it can be that stupid."

"all it does it let you avoid the hard work of deriving a a productive and meaningful explanation by writing whatever isn’t understood off to magic"

Actually, the hard work continues. And the results continue to show complexity that should rattle anybody who is still thinking. Random DNA copy errors don't do magical things either. They just foul things up. Google it.

and the other ignorant bigot appears.

To JGC #79:

“that [should evolution ever be falsified it will be replaced or SHOULD BE replaced with some natural something, AS LONG AS that something is ANYTHING BESIDES “God did it”] doesn’t characterize my position at all.”

I don’t see how it doesn’t characterize your position.

You’re ultimately looking for, and will settle for nothing less than, a “natural” explanation for observed biological diversity.

Stated differently, you’ll settle for nothing less than an explanation for observed biological diversity that originates in a something - “nature” - whose origin you can’t explain either.

So when is God going to fix all the mistakes it made in designing humans? Did it really think that taking a quadruped skeleton and standing it up on two legs wouldn't result in some dubious tradeoffs? The problem with YEC and ID is that if there were a God, it would have to be really inept. Is that the kind of God you really want?

To Michael Fugate #81:

“Trial and error is a tried and true method to design even by humans – that is natural selection in a nutshell.”

The only benefit of trial and error with humans is that the humans LEARN FROM the ERROR, and adjust their actions appropriately.

But natural selection doesn’t learn, it doesn’t even have a brain. [And I’d say NS doesn’t even exist. It’s just another word for “some things survive and reproduce.”]

If an organism mutated an eyeball under its armpit, that’s too bad. He dies with one sweaty and pretty useless eyeball. But his observant buddy [not to be confused with an “observant Jew”] can’t think, “Hey, I got a better idea. I’m gonna mutate an eyeball elsewhere, and I think I got just the place! In fact, I’m gonna double down and mutate two of them.”

Well, maybe it’s possible his buddy would THINK that, but he really couldn’t DO anything about it. And he dies eyeless.

Bottom line, I think it’s invalid, even ridiculous, to claim “natural selection” practices and even designs by “trial-and-error”. Ain’t no learnin’ goin on.

To Michael Fugate #87:

“So when is God going to fix all the mistakes it made in designing humans? Did it really think that taking a quadruped skeleton and standing it up on two legs wouldn’t result in some dubious tradeoffs? The problem with YEC and ID is that if there were a God, it would have to be really inept. Is that the kind of God you really want?”

Michael, how about we establish this ground rule for this thread STARTING NOW:
NO discussion of, or questions about, gods or God or religion; such subjects are out of bounds for this thread.

Agreed, Michael?

How about the rest of you out there?

Agreed?

"How about we establish this ground rule for this thread STARTING NOW: NO discussion of, or questions about, gods or God or religion; such subjects are out of bounds for this thread."

Sweet music to their ears!

“So when is God going to fix all the mistakes it made in designing humans?”

That happens at the resurrection for those who will be attending.

Actually, whales aside, humans seem to outlive just about every other mammal by a wide margin. Granted, we rarely attain the grace and dignity of my Rottweiler (do you know what’s black and brown and looks good on a democrat?), but most dogs don’t usually live nearly long enough to vote.
-
“…taking a quadruped skeleton and standing it up on two legs wouldn’t result in some dubious tradeoffs?”

I keep telling you to spend some time and find out what mutations are really all about. Do you really think that introducing 100 new errors every time a genome is duplicated is moving mankind upward and onward?

I see that See Noevo, whoever he, she, or it is, has successfully hijacked a thread that's supposedly about Darwin's Doubt and the Cambrian explosion. Pity.

John Harshman,

Well, rather than a lamentation, could you type your own assessment of the Cambrian explosion? We know about the forms. Wikipedia says that it lasted “for about the next 20–25 million years, [and] it resulted in the divergence of most modern metazoan phyla”. That’s interesting enough, but the more intriguing explosive aspect is the genetic information involved. What would you attribute that to? What leads you to believe that DNA replication errors could do it? When do you suppose the replication enzymes came into play? Would you think those were helpful in the explosion, or an obstacle?

I googled “evolution and medicine” and found some very quickly. SN’s not even trying.

He redefines the term. It's all* been done before. He's Gumby, dammit!**

P.S. This could use a tune-up for newer Greasemonkeys (etc.), but it still works, if anyone's looking for a killfile.

* OK, the parameter space hasn't been completely searched, but still.
** Ask him about loop quantum gravity.

To John Harshman #92:

“The Cambrian Explosion is just the hook to get you interested, and it takes up the first few chapters [of Stephen Meyer’s book “Darwin’s Doubt”] …
But the take-home message is that no matter how long you give evolution, no significant change can take place. So the whole thing about the fossil record, shortness of the Cambrian explosion, etc. is irrelevant. Evolution is just impossible.”

Interesting.
Please tell us more about the details of this take-home message.

https://www.youtube.com/watch?v=WoXzF9zDy_k

“It is the kind of question only a creationist would ask in that way, and it was the point I tumbled to the fact that I had been duped into granting an interview to creationists – a thing I normally don’t do, for good reasons.”

Right you are Richie. Your used to being coddled by minions and lackeys. (Technically, minions rank lackeys, I think.)

To Phil #96:

I’m not sure but I don’t think Richie even attempted to answer the one question posed to him:
“Can you give an example of a genetic mutation or an evolutionary process which can be seen to increase the information in the genome?”

You must be quote mining Dawkins. I mean, video mining Dawkins.

Shame on you!

But Richard sure APPEARS to be a thoughtful guy. That was quite a thoughtful pause at 0:12-0:34.
And then he proceeded to not answer the question.

Please tell us more about the details of this take-home message.

HIV-1 can't turn into a kitten. He's a rank baraminologist.

I apologize, but I think responding to either See Noevo or Phil would be counterproductive.

WTH.

“Can you give an example of a genetic mutation or an evolutionary process which can be seen to increase the information in the genome?”

Can you define "information"?

This is a bit of topic, but at least it’s not violating my proposed ground rule in #89.

A nearby article is titled “Are pigs really like people?”

I posted a comment there which is “awaiting moderation”, as all my comments initially seem to be on Greg Laden articles.

In case it never makes it over there, here it is:

I was thinking maybe pigs aren’t like people because they have 48 chromosomes, while humans have 46.

But then, chimpanzees have 48 chromosomes, and we’re said to share a common ancestor.

As I write this, I’m smoking a cigar, a Padrón, no less. And coincidentally, I noticed that tobacco has 48 chromosomes.

So, maybe I’m smoking my distant relative.

http://en.wikipedia.org/wiki/List_of_organisms_by_chromosome_count

SN,

He can’t answer that because gene damage events cannot possibly produce new and more sophisticated information.

The big deal really has nothing to do with creation/evolution issues. It is about education. The TOE comes with a dogma, and rules, and these are taught, learned, observed and enforced. All the canned answers, all the jargon, all the escape hatches. That’s why we hear the constant squeal and appeal to natural means and methods. Whether or not natural proposals are rational does not matter. The rules matter. It isn’t about the truth. It is about mind-blowing conformity.

John Harshman,

"I apologize, but I think responding to either See Noevo or Phil would be counterproductive."

No need to apologize. John. There is no shame in walking point with a loser platoon.

John Harshman said:

"I suppose it’s time for everyone who wants to talk about the supposed “sudden appearance” of the Cambrian fauna to google “small shelly fauna”,"

Steve Meyer's primary position
Is to practice the lies of omission
He omits the small shelly fauna
Don't say that I didn't warn ya

He can’t answer that because gene damage events cannot possibly produce new and more sophisticated information.

You're putting the cart before the horse. He has just conceded that the best he can do in terms of actually explaining his imaginary Gotcha! moment is to define "information" as "number of chromosomes."

Again, rank baraminology.

Is there a reason that ERVs are silenced? Oh, wait, not "The Genome." Gain or loss of function has just been asserted to be Not Information, much less have feedback effects. Proteins? Not Information. Etc.

John Harshman is mostly right, but I'd invoke the metaphor of the two temperature ranges suitable for safe food handling and storage.

Christine, that rhyme doesn't work unless you say it with an English accent.

Random DNA copy errors don’t do magical things either. They just foul things up. Google it.

Yeah, 'foul things up' like a single point insertion mutation creating a new open reading frame which expresses a novel protein capable of digesting nylon oligomers, conferring such an increase in relative fitness that in a few generations it becomes fixed in the population and results in the production of an entirely new strain of bacteria with a unique phenotype,

Flavobacterium K172. Google it.

You’re ultimately looking for, and will settle for nothing less than, a “natural” explanation for observed biological diversity.

"Supernatural explanation" is an oxymoron, See--writing what isn't understood off as "It all happened by magic at the direction of my invisible friend--you know, the one with all the neat superpowers" doesn't explain anything.

To John Harshman #99:

“I apologize, but I think responding to either See Noevo or Phil would be counterproductive.”

Touché, John.

You must have been on the debate team in high school, or maybe elementary school. Perhaps you won many a battle by default, with the other side not showing up.

But I show up.

Oh, you’re not technically squelching debate, of course. And certainly not advocating I be silenced. At least not yet.

Rather, you’re squelching with silence – yours. Taking your marbles and going home.

Hey, it’s a free country, or free internet. At least for the time being.

Tonight someone sent me an article whose topic is not directly relevant to the Cambrian Explosion, but it does touch on the free exchange of ideas, which is supposedly what sites like this are about. I liked it very much. See what you think.

Excerpts from an article titled “Building the New Dark-Age Mind” [I’ve added some commentary in brackets.]

“There was more free speech and unimpeded expression in 5th-century Athens than in Western Europe between 1934-45, or in Eastern Europe during 1946-1989. An American could speak his mind more freely in 1970 than now. Many in the United States had naively believed that the Enlightenment, the U.S. Constitution, and over two centuries of American customs and traditions had guaranteed that Americans could always take for granted free speech and unfettered inquiry.

That is an ahistorical assumption. The wish to silence, censor, and impede thought is just as strong a human emotion as the desire for free expression — especially when censorship is cloaked in rhetoric about fairness, equality, justice, [and See Noevo would add “science”] and all the other euphemisms for not allowing the free promulgation of ideas.

George Orwell devoted his later years to warning us that while the fascist method of destroying free expression was easily identified (albeit only with difficulty combatted), the leftwing totalitarian impulse to squelch unpopular speech was far harder to resist — couched as it was in sloganeering about the “people” and “social justice” [and See Noevo would add “science”].

… But if a bookend Professor B in the same venues announced that he found Muslim groups equally suspect, or that, due to constant deprecation of white males, he was holding tutoring sessions only for his European-American students, or that he was hosting a campus conference on the unscientific nature of the global warming movement [and See Noevo would add “the evolution movement”], or if he urged the university to insist that any allegations of rape follow strictly the rules of evidence and procedures as outlined in the U.S. Constitution and state laws of criminal jurisprudence, he would find himself in a great deal of trouble, if not fired.

… Current popular culture is not empirically grounded, but operates on the premise that truth is socially constructed by race, class, and gender concerns [and See Noevo would add “and the premise that truth is “scientifically” constructed by evolutionists.”].

… Science, logic, probability, evidence — all these cornerstones of the Enlightenment — now mean little in comparison to the race, class, and gender [and See Noevo would add “evolutionary science”] of those who offer narratives deemed socially useful.

… In our current Dark Age, logic is ignored in lieu of ideology.

… This descent into the Dark Ages will not end well. It never has in the past.”

http://pjmedia.com/victordavishanson/building-the-new-dark-age-mind/?si…

"Christine, that rhyme doesn’t work unless you say it with an English accent."

It's a tribute to Stephen's Cambridge PhD thesis on the issue.

Phil B wrote:

This blog is generally excellent, and over the years has provided some first rate discussions with many useful contributions from numerous sources.
Sadly, it seems that there is now some threat to this fine tradition. Jason’s commitment to allow free expression in so far as this is reasonable is admirable, and he should certainly be supported in this by his contributors. However, it also behoves those contributors to be equally reasonable in return, and in this respect there does now seem to be a problem.
Nobody can object to contrary views being freely and honestly expressed, but in recent months we have witnessed the blog being assaulted – one might say trolled – by a few contributors. They know who they are, but the most egregious culprit (at least over recent posts) is undoubtedly the individual who styles himself “See Noevo” (which he surely doesn’t, and won’t).

...Can I please implore dean, Michael Fugate, Alex SL and others to desist from encouraging this truculence? You really are just battering your heads against a brick wall, which ends up being greatly detrimental to the blog as a whole. Given Jason’s generally open generosity in putting up with a great deal of aggravation in the name of free speech, can we not agree to help him out by refusing to take long trips down blind alleys?

Well said! As I've said many times, I hate banning people and have only done so in the past under the most extreme circumstances. My general policy is to let anyone, even trolls, say whatever they want, so long as they conform to some minimal standards of good taste. If other folks want to engage the trolls that's their business. But I do wish some of the more reasonable commenters around here, you know who you are, would either stop engaging them altogether, or at least cut off the conversation after a few rounds.

See Noevo--

As I've said before, I've been more than generous letting you comment here. I even let you comment under a pseudonym. But, and I'm asking you nicely for now, please keep in mind that you are a guest in my house. I'm fine with critical comments, even one's I think are silly. Your commenting has become so relentless, however, that you seem to think these threads exist solely as your own personal soapbox. I'm a little tired of seeing my “Recent Comments” bar filled up with your name. Yesterday you left seventeen comments on this thread. You don't think that's a little excessive? So please limit yourself to one or two comments per day. OK? I don't think that's unreasonable. You can say what you want to say without replying to every comment directed at you. You need to learn the art of letting things drop.

See Nuevo "Tonight someone sent me an article whose topic is not directly relevant to the Cambrian Explosion, but it does touch on the free exchange of ideas, which is supposedly what sites like this are about."

But the only contribution that *you've* made to the discussion of the "Cambrian Explosion" is lame quote mines.

Also, please note that "unfossilized soft tissue" has never been found in any fossil. Fossilized remnants of soft tissue, yes. Just like fossilized bones and teeth are remnants of (mostly) hard tissues. Organismal tissues can and do fossilize --- hard tissues are more likely to fossilize than soft ones, but it's all just tissues. Plant leaves fossilize ---that's soft tissue. The bodies of the Burgess Shale animals are soft tissue. Etc. etc.

The main reason why we are now finding new types of fossilized soft tissues (e.g., remnants of blood cells) is because we have the technology to detect them.

It would help your arguments if you got your arguments from the scientific articles, not from sensationalist press releases or creationist websites.

There's a number of natural mechanisms which have been observed to create new genetic "information", See, such as gene duplication followed by mutation of the duplicated gene (such as contributed to the development of the clotting cascade and bacterial flagellum).

Rather, you’re squelching with silence – yours. Taking your marbles and going home.

Sound ironic?

"I probably shan’t return here. I’m getting going over at
h[]tp://scienceblogs.com/evolutionblog/2015/06/10/the-cambrian-explosion/#comment-63431"

I think there's an approprate capsule summary of the underlying psychology.

To Jason Rosenhouse #111:

I hear you. I’ll try harder to limit the number of my posts in the future.

In the interest of equity, I do hope you send a similar warning to some others at this site.
For instance, I just took a quick look back at http://scienceblogs.com/insolence/2015/05/20/why-do-doctors-deny-evolut…
and noticed that a pseudonym “Narad” had 14 posts on May 21 alone, and a pseudonym “ann” had 16 posts on May 28 alone.

In the interest of equity, I do hope you send a similar warning to some others at this site.

QED.

I'll be watching from the sidelines henceforth.

To Jason Rosenhouse #111, part 2:

Last comment for the night, I promise.

I looked back again at http://scienceblogs.com/insolence/2015/05/20/why-do-doctors-deny-evolut…

I was REALLY active on that one!

I was responsible for approximately 214 posts, over 14% of the 1,485 comment total.
I thought it was going to be closer to 20% or more, but it wasn’t even 15%. But that’s a good thing, I guess.

Is 1485 comments a record, or close to a record, for an article here?

Oh dear. Having gone to bed with comment numbers in the early 80s, I awake to find numbers at 117 – our old friend having precipitated much of the extraneous garbage, now assisted by 1 or 2 co-conspiratorial henchmen. Yet again a good post, in which several knowledgeable people have contributed usefully to a discussion of the CE and Meyer’s perverse views thereof, has been hijacked - with many of those same useful contributors nevertheless continuing to feed the dog, ensuring that he keeps coming back for more at every turn.

Jason – I note your warning to SN at #111. However, might I point out that my initial appeal was not to SN (he’s surely incorrigible, as his own link to a blog on which he posted over 200 times will pretty thoroughly demonstrate), but to his respondents. They are all, no doubt, well-motivated, but they seem unable to resist rising to the bait, and the end effect is just to encourage the very behaviour to which we’re all objecting in the first place. I took on board eric’s suggestion that a decent exchange can nevertheless take place above and around such distractions but, even so, it would all be a lot better without. The solution, as I suggested before, lies not in the hands of SN etc., and hopefully not by forcing you to ban people. What we all need to do, as earlier stated, is to stop feeding the dog. As long as he fails to get responses from informed individuals, then there must be a chance that he will be less amused by his own game, and who knows – perhaps even desist, as you have asked, and as he has hinted he may actually do at #115. Might I respectfully suggest that your admonitions be aimed not so much at SN himself, but at those who persistently respond to whatever nonsense he feels disposed to produce?

Phil B --

It seems to me I did scold both sides. I think See NoEvo should rein in his relentless commenting, and I think others should not feel that they must always rise to the challenge of trying to refute him.

Point taken. Let's just hope it has some effect - on both sides of the equation.

Well, I can say there's an upside to our over-night power outage; I was not tempted to participate in the mud wrestling.

And if I can change the subject (back to the original posting): ID is dead--as a scientific concept. The ID movement is obviously alive, tho' it's efforts are devoted to flogging its dead horse and cursing those whose horses run on.

sean s.

@SN, 101:
And there are some people with fewer chromosomes than you, so they are less related to you than tobacco, right?

http://www.ncbi.nlm.nih.gov/pubmed/6510025

Chromosome numbers can change in evolution. And BTW, your mind is a gift by god in Roman Catholicism, so wasting it is a since. Or, in shorter terms, next time you post, try to read up on cytology...

SN @101: PRATT.

I felt like I said what I wanted to say (at least to the handful of people who read the book)
Now you are making me feel bad that I just read this book from the library instead of buying it :(

@99 JH: "I think responding to either See Noevo or Phil would be counterproductive."
There is only one way to make discussing denialists like SN and Phil (they never have brought up any positive evidence themselves for their god creating whatever kind of stuff, only theology) counterproductive is by mocking them and pointing out their lies. Then they provide entertainment.
Any attempt to a serious discussion can only be a waste of time.

Regarding #125

I can’t speak for others, but I don’t come here for the entertainment. Sorry Professor, but there are other venues I prefer for that. If entertainment is the only reason to engage SN and Phil, then there’s No Reason, imho.

sean s.

I have to agree with sean at #126. Entertainment is not a good reason for engaging these guys - unless you're the sort who's entertained by observing a car crash.

Meanwhile, sean, you seem to be enjoying the liberal use of your new found acronym! Glad to be of service.

So, then, what is the Cambrian explosion? My opinion, and it is my own, is that it's largely a taphonomic artifact: the coincidence (at least I can't think of a causal connection) that a particular sort of preservation -- the Burgess/Chengjiang type that resulted in soft-bodied Lagerstätten -- and the origin of calcified skeletons in large animals happened at almost the same time. The real increase in diversity happened some time before we see any very good evidence of its nature, and this is shown by the small shelly fauna and ichnofossils. The "explosion" begins in the latest Ediacaran and ends around the beginning of Cambrian Stage 3 (i.e when we first see all that diversity), a period of around 25-30 million years, mostly invisible to us.

JGC,

“There’s a number of natural mechanisms which have been observed to create new genetic “information”, See, such as gene duplication followed by mutation of the duplicated gene…”

There are very good reasons to doubt this. Gene duplication is a giant error in itself, and claims about subsequent errors making a reckless copy do something else are, by and large, just claims. Even small genomes are very large. The odds obviously do not favor specific errors occurring in just the right place. The odds do not favor fixation. And the odds sure as hell do not favor this idiotic scenario happening billions of times. Use your head.
-
“(such as contributed to the development of the clotting cascade and bacterial flagellum).”

It isn’t hard to determine what you read.

Go find one of the diagrams showing the specific proteins in the flagellum, like this one:
http://www.nature.com/nrmicro/journal/v6/n6/fig_tab/nrmicro1887_F2.html
You will notice (very presumptuous on my part) the components tagged with boxes. Do a search, and type in any of the Fl proteins you see. They are all very specialized.

You need to do some thinking (and some normal reading) about hyper-complex, proton-driven machines. Things like this occur accidentally only in mindless minds. Use your freakin head.

Michael Fugate,

“If the creationists here really were as intelligent as they claim and really wanted to make a difference, they would go back and get retrained in biology, geology or astronomy and set out to test their hypotheses (if they have any) in a rigorous manner.”

Test the hypotheses? What tests do you apply? ‘Testing’, like ‘empirical’, is a word that means something. Just having a letter sequence in your vocabulary does not mean that you test anything. Your training has taught you about how not to test, and feel good about your failure to test.

The object of the game is to arrive at the truth Michael.

With comment 130, a tu quoque argument, my bingo card is full.

There are very good reasons to doubt this.

Idnetify those reasons, please--I failed to find any such in your post.

Gene duplication is a giant error in itself

Why are you characterizing 'change' as 'error'? By what rational argument can a change that will result in increased fitness be considered an error?

... and claims about subsequent errors making a reckless copy do something else are, by and large, just claims.

This is not a claim but something we've observed to have occurred (recall again the elements in the clotting cascade which arose by this mechanism).

Even small genomes are very large. The odds obviously do not favor specific errors occurring in just the right place.

There is no necessity that genetic changes occur in "just the right place", however. Changes that occur in any location that confer increased fitness wth respective to environment are selected for, that's all.

The odds do not favor fixation.

One a change occurs that confers a significant increase in fitness we're no speaking in terms of 'odds'--natural selection operates in a non-random manner.

And the odds sure as hell do not favor this idiotic scenario happening billions of times.

What makes you think gene duplication followed by subsequent mutation must happen 'billions of times' to generate genotypes resulting in increased fitness, such that natral selection results in the new allele becoming fixed in the population? Show your math.
“(such as contributed to the development of the clotting cascade and bacterial flagellum).”

Do a search, and type in any of the Fl proteins you see. They are all very specialized.

I suggest you do a search typing in "Type III Secretory System", where you'll see that the proteins forming the base of the flagellum are analogs of proteins forming a structure bacteria use to translocate toxins through the cell membranes of their host's cells.

You need to do some thinking (and some normal reading) about hyper-complex, proton-driven machines. Things like this occur accidentally only in mindless minds.

Evolutionary models don't state or predict that systems like the bacterial flagellum arose accidentally, Phil.

Use your freakin head.

I am--that's why I've rejected your argument.

a man who thinks that the earth is 6000 years old is calling millions and millions of scientists idiots - rich!

JGC,

“Why are you characterizing ‘change’ as ‘error’?”

Because it is an accurate characterization. You will find the word used at least a dozen times here: http://www.nature.com/scitable/topicpage/dna-replication-and-causes-of-…

Mutations are copy failures. There are extremely efficacious replication enzymes which are there to maintain genetic fidelity and stability. In other words, they serve specifically to prohibit the evolutionary process which depends on failures.

How and why would you suppose these enzymes ‘evolved’?
-
“This is not a claim but something we’ve observed to have occurred (recall again the elements in the clotting cascade which arose by this mechanism).”

This is just what you’ve been told. Let me point out that “we” has not observed anything but a functioning system. The arose part is conjecture. Accidents do not result in precision and function.
-
“There is no necessity that genetic changes occur in “just the right place”, however.”

What? If you have a duplicated gene, the mutations that are supposed render it into neofunctionality have to occur in that gene.
-
“What makes you think gene duplication followed by subsequent mutation must happen ‘billions of times’..[?]”

Millions of extant and extinct species means billions of biological definitions, which is information, which resides in genes. The genes have to come from somewhere.

Gene duplication is the only available shortcut for building genes and gene families, which is why the concept is sanctified and beloved. The only alternative is building from absolute, accidental scratch.
-
“the proteins forming the base of the flagellum are analogs of proteins forming a structure bacteria use to translocate toxins through the cell membranes of their host’s cells.”

This is nonsense in a tuxedo. It does not cover the number of, or the exquisite function specialized proteins that serve as clutches, rotors, stators, bearings, etc. in flagellum motors. How do you account for these?
-
“Evolutionary models don’t state or predict that systems like the bacterial flagellum arose accidentally”

Then those models are ignoring the workhorses of the new synthesis. Unless you accept something like directed mutagenesis, evolution depends on accidents.

“a man who thinks that the earth is 6000 years old is calling millions and millions of scientists idiots”

Not really, Michael. Anybody can be trained to steer around very basic questions in order to preserve religious ideas. You demonstrate that quite well, and I can illustrate that by asking one. How, and why, did replication enzymes originate?

Also, the particular scientists you are referring to probably believe the space particles/deep sea vent fairy tales. So I’m not awed by the consensus you revere.

As for the 6000 years, endogenous biological material in fossils entirely supports my beliefs, but it is yet another turd in your punchbowl.

@Colnago80

Thanks for the suggestion. SN is now killfiled. Unfortunately, that doesn't stop me seeing replies to him, so let's hope others will kf him too. Or I may just kf the most frequent responders.

Phil, how and why do you believe replication enzymes originated? Be specific.

I trust your explanation takes some form other than "By magic, at the direction of my invisible friend--you know, the one with all the neat superpowers."

John @128:

So, then, what is the Cambrian explosion? My opinion, and it is my own, is that it’s largely a taphonomic artifact: the coincidence (at least I can’t think of a causal connection) that a particular sort of preservation — the Burgess/Chengjiang type that resulted in soft-bodied Lagerstätten — and the origin of calcified skeletons in large animals happened at almost the same time.

I can't help but think that the development of 'hard parts' could've touched off an arms race, leading to a (relatively) large increase in new forms in a (relatively) short time. So I don't think its entirely artifact. Maybe something more like an invasive species that comes in, wipes out the competition, and then diversifies in the ecological niches that previously had soft-bodied occupants but which are now comparatively empty.

Phil:

Gene duplication is a giant error in itself,

Once you admit duplication occurs, you've already accepted that that random mutation can increase genomic information using measures like -Log(p) and Shannon information. -Log(p) is, IIRC, what Dembski and other ID creationists use, so even they use a definition of information under which duplication increases it. Though I've occasionally heard quotes from creationists that seem to deny this, there's never any math behind it. I think it would be pretty hard to construct a definition of information in which 'desert' and 'dessert' contain the same information.

And everyone knows you get more points in Scrabble™ and Boggle™ for spelling dessert instead of desert. Take that Dembski!

I can’t help but think that the development of ‘hard parts’ could’ve touched off an arms race, leading to a (relatively) large increase in new forms in a (relatively) short time. So I don’t think its entirely artifact.

Not entirely, perhaps. But hard parts, as displayed in the small, shelly fauna, accumulate gradually over the course of 25-30 million years before we see the first fully armored, calcified fossils (trilobites, mollusks, brachiopods). So not so much of an explosion.

There are other related explanations that have been suggested: the invention of macropredation and of eyes. Eyes being not that all preservable, no evidence of their existence shows up until the Chengjiang. And evidence of macropredation would mostly rely on body fossils, again with nothing clearly shown until Cambrian Stage 3. Though there are claimed drill holes in some Ediacaran fossils.

Agree with your first part. Was unfamiliar with 'macropredation' and a quick google turns up links mostly about lions and tigers...but I assume you mean predation by organisms that are not microorganisms?

Macropredation is predation by and on organisms that aren't microorganisms.

My favorite demonstration that "accidents can produce information" is genetic algorithms we use all the time to solve difficult problems, even engineering problems like airplane wing design. More properly we'd say that these algorithms operate on "errors" in phenotypic replication rather than genetic, which makes them orders of magnitude simpler than the kinds of interactions available in actual genetic trial-and-error.

A really fun one is BoxCar 2D, which sets up a toy world of 2-dimensional cars that traverse a terrain, and which replicate with mutation and "mating." They start off mostly immobile, but eventually a mutation will stick and allow a car to move forward. As you watch things progress, what you find out is that the information being generated is about the terrain itself: features of the terrain are encoded into the design of the cars that go the furthest.

To John Harshman #140:

“There are other related explanations that have been suggested: the invention ...of eyes.”

“Invention”? Darn those inappropriate metaphors! I guess you evolutionists just can’t stop yourselves from using that g d design language.

Also, you would have done at least a LITTLE better if you had said “inventionS” of eyes. I mean, let’s not forget about “convergent” evolution.

The eye thing is really interesting, because Marty "See Noevo" K. has already admitted he can't identify any specific problems with the content at Lindsay's web site. That tells you all you need to know.

SN, do you consider yourself "highly intelligent?" Don't be afraid of giving a direct answer.