The Cambrian Explosion and DNA

nacker
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The Cambrian Explosion and DNA

I know I know... this is from one of evolutions antichrists (Discovery Institute), but it is a well cited, scientifically logic, and educational paper on the Cambrian Explosion.

Basically it looks at the complexity of additional genetic information in the DNA of the multiple phyla exploding on the scene of life at the Cambrian Explosion, shows the weaknesses of present theories and offers its own.

http://www.discovery.org/articleFiles/PDFs/Cambrian.pdf

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


Yellow_Number_Five
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Re: The Cambrian Explosion and DNA

nacker wrote:
I know I know... this is from one of evolutions antichrists (Discovery Institute), but it is a well cited, scientifically logic, and educational paper on the Cambrian Explosion.

Basically it looks at the complexity of additional genetic information in the DNA of the multiple phyla exploding on the scene of life at the Cambrian Explosion, shows the weaknesses of present theories and offers its own.

http://www.discovery.org/articleFiles/PDFs/Cambrian.pdf

I'm not reading a 50 page paper from the Discovery Institute to satisfy your personal gripes. Why don't you sum it up for us, if you've actually read it yourself.

Why do I have the feeling this is going to fall under the logical fallacy that a challenge for evolution=proof of God?

I am against religion because it teaches us to be satisfied with not understanding the world. - Richard Dawkins

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The Cambrian Explosion and DNA

It certainly isn't because it's damn obvious it will... is it?


nacker
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The Cambrian Explosion and DNA

I'll get right on the summary. I'll try to have some time early-mid next week.

And let's go ahead and settle this part of our discussions...

I am a theist.
You are not.

Cool.

Now you don't have to end every post by, "And now you'll probably say something about God," or what ever.

Are we talking about evolution and the evidence for and against it??? then let's talk about it. If at some points I feel the evidence is pointing to design or more specifically to creation I'll say it. Now you don't have to anticipate it anymore. And not once in our discussions have I said that the destruction of one scientific theory will automatically push anywhere but to that destruction. Stop stereotyping, generalizing, and character bashing.

And ridiculing a person's ideas from your own naturalistic presuppositions is not a logical argument. Or really rational for that matter. Can we have a rational discussion now?

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


Yellow_Number_Five
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The Cambrian Explosion and DNA

nacker wrote:
I'll get right on the summary. I'll try to have some time early-mid next week.

And let's go ahead and settle this part of our discussions...

I am a theist.
You are not.

Cool.

Now you don't have to end every post by, "And now you'll probably say something about God," or what ever.

Yes, I gauantee that you will. Do you have another explanation in mind?

Let's be blunt here, you not only need to refute evolution, you need to provide a more cogent, lucid and more comprehensive SCIENTIFIC answer. Saying this cannot be, therefor it is God will not cut it.

Quote:
Are we talking about evolution and the evidence for and against it??? then let's talk about it. If at some points I feel the evidence is pointing to design or more specifically to creation I'll say it. Now you don't have to anticipate it anymore. And not once in our discussions have I said that the destruction of one scientific theory will automatically push anywhere but to that destruction. Stop stereotyping, generalizing, and character bashing.

Stop playing the martyr. We all know why you are here.

Quote:
And ridiculing a person's ideas from your own naturalistic presuppositions is not a logical argument.

No, it's ridicule. I play nice with most people, you're not one of them.

Quote:
Or really rational for that matter. Can we have a rational discussion now?

Whenever you get around to posting something that warrants that, sure.

I am against religion because it teaches us to be satisfied with not understanding the world. - Richard Dawkins

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The Cambrian Explosion and DNA

Yellow_Number_Five wrote:

Stop playing the martyr. We all know why you are here.

Quote:
And ridiculing a person's ideas from your own naturalistic presuppositions is not a logical argument.

No, it's ridicule. I play nice with most people, you're not one of them.

Quote:
Or really rational for that matter. Can we have a rational discussion now?

Whenever you get around to posting something that warrants that, sure.

"Stop playing the martyr. We all know why you are here." Man... that response was exactly what the section you responded to was saying in the first place. You are stereotyping me because I'm a theist. Your bigotted and prejudiced answers are an argument against your role as a rational responder. You've turned your atheism into a new sort of racism where you find it acceptable to generalize about someone you've never met, and attack my character just because I'm not like you. No one is playing the martyr... but you are playing the tyrant. Not once in my posts have I attacked anyone personally, or ridiculed them. I find it interesting that I am having to spend time on this forum asking the moderator to stop attacking me and to have calm discussions. You are sounding like the thing you hate.

Please... let's start talking about things that really matter.

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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The Cambrian Explosion and DNA

I clicked on the link for this with the understanding that there would be some kind of case against evolution, but it seemed to be a rant by a theist who is bitter because he seemingly has no case for his views. All yellow asked was for a summary, not for you to rant and rave about the stereotyping that "rational theists" face. If you have a case, present it. Nothing in the article really suggests any one conclusion. It merely presents the same general argument that evolution is not 100% certain, and it DOES indeed propose that this uncertanty suggests design, which is the conclusion that yellow made and you lashed out against. Maybe if you don't want to be stereotyped next time, DON'T FIT THE MOLD OF THAT FUCKING STEREOTYPE.

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The Cambrian Explosion and DNA

Mr. Apples,

You are correct. I should have pre-empted the link with the acknowledgement that since it came from discovery... that it would present a case for ID. Although I did assume that would be fairly obviouse I should have stated that I was more interested in the case it makes against evolution than the case for ID. Thank you for your educated, brilliant, and wonderful oration.

Hopefully the summary will be posted tomorrow for more rational discussion.

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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The Cambrian Explosion and DNA

nacker wrote:
Mr. Apples,

You are correct. I should have pre-empted the link with the acknowledgement that since it came from discovery... that it would present a case for ID. Although I did assume that would be fairly obviouse I should have stated that I was more interested in the case it makes against evolution than the case for ID. Thank you for your educated, brilliant, and wonderful oration.

Hopefully the summary will be posted tomorrow for more rational discussion.

Rationality and Intelligent Design in the same discussion? Maybe those arguing against it.

'We are all atheists about most of the gods that societies have ever believed in. Some of us just go one god further.' - Richard Dawkins
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The Cambrian Explosion and DNA

OpiateCopulation wrote:
nacker wrote:
Mr. Apples,

You are correct. I should have pre-empted the link with the acknowledgement that since it came from discovery... that it would present a case for ID. Although I did assume that would be fairly obviouse I should have stated that I was more interested in the case it makes against evolution than the case for ID. Thank you for your educated, brilliant, and wonderful oration.

Hopefully the summary will be posted tomorrow for more rational discussion.

Rationality and Intelligent Design in the same discussion? Maybe those arguing against it.

aaaannnnnd. two points for you.

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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The Cambrian Explosion and DNA

This is gonna be pretty long so I'm going to post it in sections. Here is section I and II.

A Summary of:

The Cambrian Explosion: Biology?s Big Bang
by Stephen C. Meyer, P.A. Nelson, and Paul Chien
by
Nacker

I. Introduction: Design Without a designer?

The article is introduced by acknowledging that Darwin himself, and neo-Darwinists of our own time ?such as Francisco Ayala, Richard Dawkins and Richard Lewontin,? have acknowledged that biological organisms appear to have been designed by an intelligence, but they will stop at its appearance.
It quotes Ayala: (See article for citation)
The functional design of organisms and their features would therefore seem to argue for the existence of a designer. It was Darwin?s greatest accomplishment to show that the directive organization of living beings can be explained as the result of a natural process, natural selection, without any need to resort to a Creator or other external agent. ....[Darwin?s] mechanism, natural selection, excluded God as the explanation accounting for the obvious design of organisms.1

Darwin?s theory did away with the necessity for accepting the designer b/c natural selection acting on random variation was a good enough explanation. The article acknowledges the explanation of natural selection acting on random variations for small scale micro-evolution but begs the question if it can account for the origin of completely new organs, body plans, and structures. This is what the paper wishes to test.

II The Cambrian Explosion
A detailed definition of the Cambrian explosion that I?ll include only as a paranthesis, assuming that it is understood (sudden appearance in the fossil record of most if not all phyla within 5 million years indicating the presence of a ?complex food web and diverse ecological community?). [see page two for the full explanation]
I found this very interesting:
?The Lower Cambrian sediments near Chengjiang have preserved fossils of such excellent quality that soft tissues and organs, such as eyes, intestines, stomachs, digestive glands, sensory organs, epidermis, bristles, mouths and nerves can be observed in detail. Even fossilized embryos of sponges are present in the Precambrian strata near Chengjiang.10 Cambrian-level strata show the soft body parts of jelly-fish-like organisms (known as Eldonia), such as radiating water canals and nerve rings. These fossils even include the gut contents of several different kinds of animals and undigested food residue in their stools.11? Page 3, 4

?The major body plans that arise in the Cambrian period exhibit
considerable morphological isolation from one another (or ?disparity?) and then
subsequent ?stasis.?? 4

?the emergence of the Ediacaran biota (570 million years ago), and then to a much greater extent, the Cambrian explosion (530 million years ago) represent steep climbs up the biological complexity gradient. Indeed, analyzed from an information-theoretic standpoint, the Cambrian explosion in particular represents a remarkable jump in the (specified)18 information content of the biological world.?

More complex, multi-cellular organisms would require new cell types which would require specialized proteins, which require more genetic information encoded in DNA.

?For example, molecular biologists have recently estimated that a minimally complex cell would require between 318 to 562 kilobase pairs of DNA to produce the proteins necessary to maintain life.20 Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require an amount of DNA greater by several orders of magnitude (e.g., the genome size of the worm Caenorhabditis elegans is approximately 97 million base pairs21 while that of the fly Drosophila melanogaster (an arthropod), is approximately 120 million base pairs.22 For this reason, transitions from a single cell to colonies of cells to complex animals represent significant (and in principle measurable) increases in complexity and information content.? 5

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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The Cambrian Explosion and DNA

Natural selection when observed and looked back upon shows signs of design, yes. That design though is nothing more than natural selection itself. Our perspective creates the illusion of a designer when actually the function of natural selection is all that was present.

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The Cambrian Explosion and DNA

III. Testing the Neo-Darwinian and Punctuated Mechanisms.
.The authors will study the efficacy of neo-Darwinism and punctuated equilibrium as explanations for the Cambrian explosion because:
?(a) neo-Darwinism especially purports to offer a truly creative mechanism of biological change and because (b) the Cambrian fossils attest not only to small-scale variations but also to large scale innovations in basic body plans, the Cambrian data provide a key test of the efficacy of neo-Darwinism?s mutation/selection mechanism.?

III. A.) Prediction 1: The Gradual Emergence of Biological Complexity and the Existence of Numerous Transitional Forms Leading to Phyla-Level Body Plans

?Given the operation of the neo-Darwinian mechanism, the fossil record should show: (1) the gradual emergence of biological complexity and the existence of numerous transitional forms leading to new phyla-level body plans; (2) small-scale morphological diversity preceding the emergence of large-scale morphological disparity; and (3) a steady increase in the morphological distance between organic forms over time and, consequently, a steady increase in the number of phyla over time.?

As Susumo Ohno has explained:
Assuming a spontaneous mutation rate to be a generous 10-9 per base pair per year and also assuming no negative interference by natural selection, it still takes 10 million years to undergo 1% change in DNA base sequences. It follows that 6-10 million year in the evolutionary time scale is but a blink of an eye. The Cambrian explosion denoting the almost simultaneous emergence of nearly all the extant phyla of the Kingdom Animalia within the time span of 6-10 million years can?t possibly be explained by mutational divergence of individual gene functions.25 page 7

?since the variation/selection mechanism involves a trial and error process, both Darwinism (and neo-Darwinism) imply that the fossil record should show many transitional organisms and failed experiments.?
?Instead, organisms such as Trilobites (Phylum Arthropoda), with their articulated body plans, intricate nervous systems and compound eyes, first appear fully formed at the beginning of the Cambrian explosion along with many other phyla of equal complexity.? Page 8

Here the article summarizes punctuated equilibrium and states that the fossil record doesn?t support this theory either, although it was formed to describe the faulty record.
In light of the Cambrian explosion ?the proposed mechanism of punctuated evolutionary change simply would have lacked the raw material upon which to work.? page 9 Punctuated equilibrium would need a pool of species previous to the explosion which the fossil record does not present.
It then summarizes the work of Michael Foote of the University of Chicago on statistical paleontology that supports the work of Valentine and Erwin ?who concluded that ? neither the contending theories of evolutionary change at the species level, phyletic gradualism or punctuated equilibrium, seem applicable to the origin of new body plans? and thus, we now require ?a [new] theory for the evolution of novelty, not diversity.?? page 10.

III. B. III.B. Prediction 2: Diversity Precedes Morphological Disparity (contra
completeness and morphological breadth)

?What are the mechanisms to account for disparity? ?disparity refers to life?s basic themes, whereas diversity refers to the variations on those themes.36? page 10

I hope I do this justice? Obviously evolution does not end at the formation of new species but also accounts in the gradual formation of new genera within one family. ?Later, families will be found to have diverged to the point where taxonomists (specialists in classification) prefer to call them orders, then classes, then phyla?Ancestors of two different phyla, say vertebrates and molluscs, which we see as built upon utterly different ?fundamental body plans? were once just two species within a genus.? ? Richard Dawkins Page 10, 11.
?Punctuated equilibrium also predicts morphological diversity preceding disparity.?
The fossil record should be a cone pointing down, but looks more like the opposite. In other words, the neo-Darwinian mechanisms responsible for microevolutionary change cannot be extrapolated to explain macro-evolutionary innovation, including the origin of major body plans in the Cambrian period.

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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III.C. Prediction Number 3: The morphological distance between organic forms
and thus the number of phyla will increase gradually over time.

Stemming from III B, the models that told us natural selection acting upon random variations will result in differing phyla so the ?number of new phyla should increase in a steady logarithmic fashion as members of one phylum diversify and give rise to new phyla. Many of the phyla that first appear in the fossil record after the Cambrian are less complex than the phyla that first appear in the Cambrian. Since standard evolutionary reasoning assumes that complexity evolves from simplicity and, not generally, the reverse, many neo- Darwinists and punctuationalists have assumed that these simpler phyla must have been present in the Cambrian. Values ranging from 60% to 95% of all phyla are consistent with existing data. Though we are skeptical of strictly presuppositionally driven arguments, we do favor, on geological and environmental grounds, estimates that tend toward the mid to high end of this range.45? page 13

Both the sudden burst of phyla at the Cambrian explosion and the absence of the growing number of phyla leave neo-Darwinism and punctuated equilibrium wanting.

?The origin of major innovations and complexity are increasingly recognized as unsolved
problems for all fully naturalistic versions of evolutionary theory, and biologists,
especially developmental biologists, are beginning an intensive search for solutions.50
Before considering whether intelligent design should be considered in this search, we will
consider some objections to arguments that we have marshaled against the adequacy of
neo-Darwinism and punctuated equilibrium.?

The objections will come in the next post.

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IV. OBJECTIONS
IV.A. The Artifact Theory: Is The Cambrian Explosion Real?

?The search for the missing fossils in Precambrian formations all over the world resulted in universal disappointment. Maintaining Darwin?s theory, therefore, eventually required formulating ad hoc hypotheses to account for the absence of ancestral and transitional forms.?
The Artifact Theory is summarized: ?the fossil ancestors existed, but for various reasons were not preserved in an ?imperfect and biased?? fossil record. On this theory, the absence of the fossil ancestors represents ?an artifact? of incomplete sampling, a not accurate representation of the history of life. Gaps in the fossil record are apparent, not real.? page 15

The article presents many theories that fall under the artifact theory. The ancestors to the Cambrian explosion were too soft to fossilize, or were terrestrial due to tides, or existed as larva. All of these fall short in light of the fossil record. The question of the fossils were too soft was addressed ??animals such as brachiopods and most echinoderms and mollusks cannot exist without a mineralized skeleton. Arthropods bear jointed appendages and likewise require a hard, organic or mineralized outer covering. Therefore the existence of these organisms in the distant past should be recorded either by fossil tracks and trails or remains of skeletons. The observation that such fossils are absent in Precambrian strata proves that these phyla arose in the Cambrian.? page 16, 17
If you want more details of the artifact objections they are discussed on pages 15-18

IV.B. The Ediacaran/Vendian Radiation

These are fossils found all over the world dating from 565 mya to 543 mya. They don?t solve the Cambrian problem however b/c they could only represent 3 to 4 phyla, most have too many morphological dissimilarities with known Cambrian animals, and there is general disagreement on what some are. Even if they should be in the Animal Kingdom.
Other trace fossils are cited which ?consist of surface tracks and burrows, along with fecal pellets, which, though small, could only have been made by animal organisms of a relatively high degree of differentiation. Thus, some have argued that these trace fossils suggest the existence of organisms with a head and tail, nervous systems, a muscular body wall allowing creeping or burrowing, and a gut with mouth and anus.77 These inferred physical characteristics would indicate organisms of ?organ grade? complexity, above that of flatworms. Much of the discussion about trace fossils is, of course, necessarily speculative. Nevertheless, even on the most optimistic interpretation, these remains suggest the existence of no more than two or so animal body plans (of largely unknown characteristics). Thus, the Ediacaran data taken as a whole hardly establishes the existence of the wide variety of transitional intermediates that neo-Darwinism and punctuated equilibrium require ? page 19, 20

Even with these few phyla, the neo-Darwin and punctuated equilibrium models do not account for the explosion.

More objections coming.

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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IV.C.The Deep Divergence Hypothesis

?Recently, evolutionary biologists have attempted to defend neo-Darwinism against the evidential challenge of the fossil record in another way. Some evolutionary biologists have denied the explosive character of the Cambrian radiation and postulated a long period of undetected or cryptic evolution in the pre-Cambrian, beginning from a common ancestor, some 1.2 billion years ago. To support these claims, these biologists have asserted the primacy of molecular data over the evidence of the fossil record itself.? This is sometimes coupled with the ?soft bodied artifact theory.? And, they conclude, "[o]ur results cast doubt on the prevailing notion that the animal phyla diverged explosively during the Cambrian or late Vendian, and instead suggest that there was an extended period of divergence during the mid-Proterozoic, commencing about a billion years ago."83
But? As noted above, the preservation of numerous soft-bodied Cambrian animals, as well as Precambrian embryos and microorganisms (the latter dating from 3.5 billion years), undermines the plausibility of those versions of the artifact theory that invoke an extensive period of soft-bodied evolution as the reason for an absence of Precambrian transitional intermediates. Moreover, the existence of exclusively soft-bodied ancestors for hard bodied Cambrian forms remains anatomically implausible as noted earlier. A brachiopod cannot survive without its shell. Nor can an arthropod (e.g., a crab or an insect) exist without its exoskeleton. Any plausible ancestor to such organisms should have had hard body parts to fossilize, yet none have been found in the Precambrian.

The analysis of Wray et. al. has a second difficulty: it results vary dramatically from other similar sequence comparisons. In a more recent publication, Ayala et al. have recalculated the divergence times, using the same protein-coding genes as Wray et al. (but eliminating 18S rRNA, an RNA-coding gene, because of problems with obtaining a reliable alignment), and adding an additional 12 protein-coding genes. Correcting what they argue are "a host of statistical problems"85 in the Wray et al. study, Ayala and colleagues found that their own estimates "are consistent with paleontological estimates"?not with the deep divergence hypothesis. Third, all analyses of sequence data make assumptions that raise serious questions about their reliability as indicators of very ancient common ancestors. For example, all sequence analyses assume, rather than demonstrate, the doctrine of common descent. By assuming that sequence differences reflect the amount of time that has passed since different animals began to diverge from a common ancestor, molecular studies clearly presuppose that some such ancestor existed. In effect, sequence analyses calculate how long ago a common ancestor for two (or more) organisms might have existed?if one assumes that some such organism must have existed. These analyses also presuppose that mutation rates of organisms remained relatively constant throughout geological time. Both these assumptions are problematic.
You cannot assume what you are trying to prove. It begs the question.
The basic housekeeping proteins analyzed would have had little role in the origin of novel body parts.

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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Well... that is half of the paper... The rest is positive support for intelligent design. I can summarize it if you would like, but I didn't want to assume that you wanted it and didn't want to get yelled at for posting it. To help you decide if you want it or not I included an introduction and subheadings on this post.

V. EVIDENCE OF DESIGN?

Our discussion has suggested the inadequacy of the neo-Darwinian and punctuationalist mechanisms as explanations for the origin of the new organisms and body plans that arise in the Cambrian period. We have suggested that the punctuationalist model of evolutionary change also fails to explain key features of the fossil record. In this section, we now expand our critique of these models of undirected evolutionary change and propose an alternative. In particular, we want to suggest that the pattern of Cambrian fossil evidence suggests intelligent foresight, planning and design?not merely apparent design. We will argue, moreover, that the design hypothesis constitutes a better?more causally adequate?explanation than its naturalistic competitors for the salient features of the fossil record that we have analyzed above.

The article says that Intelligent design is not an argument from ignorance. It does not claim that just because we don?t know how something is working that we should write it off to design. It claims that ?biological organisms manifest distinctive features, hallmarks or positive indicators of intelligently design systems?that is, organisms possess features that in any other realm of experience would trigger the recognition of prior intelligent activity.?

Subheadings for positive support of ID
V.A. The ?Quantum? Increase in Specified Biological Information
V.B. The Persistence of Morphological Isolation or Disparity (Stasis)
V.C. An Inverted Cone of Diversity: Disparity Preceding Diversity
V.D. Sudden Appearance and Absence of Ancestral Precursors

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The fundamental problem with the line of reasoning used in the paper is this: sure, no one can argue that evolutionary theory and the theory of natural selection are incomplete. However, the fact that the writers see this uncertainty as evidence of design is an obvious bias. In the scientific sense, evidence should be taken for what the evidence suggests, meaning that it is irresponsible to begin with bias towards one idea and build the evidence around that. There currently is very little evidence that in and of itself would suggest design. The mountains of evidence in support of evolution are the reason that the majority of contemporary intellectuals and members of the scientific community support that theory. It isn't a matter of freethinkers being biased towards evolution, since that is what the evidence suggests; it is a matter of theists beginning with the unsupported idea of an omnipotent deity and searching evidence out to support that claim. The conclusion should never come before the evidence, that is just bad science and contradictory to progress. I mean no offense to you by saying this, but when someone comes out in support of a design theory, it had to have been born out of this backwards methodology and indeed deserves to be treated as just that: backwards logic. I am not detracting from the ideas presented in the paper, as they do indeed raise questions pertaining to evolution, but they in no way directly suggest design. They merely show why evolution IS indeed a theory. However, the evidence for evolution is still incredible and if any bias is to be introduced in these matters of uncertainty, it should be in the light of "how does this new evidence CHANGE our ideas about evolution" and not "how does this evidence completely DISCREDIT our ideas about evolution." It is a hard pill to swallow for theists to put the notion of a deity on the backburner until definitive evidence shows itself that would suggest design without the previous bias of belief in a deity, but it has to be taken that way for reason to prevail.

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The Cambrian Explosion and DNA

applesforadam,

I think we actually agree... at least on the fact that the ultimate goal is truth... not being right. It is really weird that we both can look at evidence and come to diff. conclusions. I think you are coming from a prejudice slant, and you think the same of me. At least we are both after truth... that's cool.

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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I don't doubt that you and the authors are both after truth, the only difference I believe is that any bias I have is based on emperical evidence, whereas yours is purely theistic. However, I also see no benefit in taking a harrassing tone with you since you at least show a willingness toward scientific evidence as opposed to simply saying "well the bible didn't tell me I came from apes so it can't be true." Keep looking, just make sure you are reading between the lines of articles like the one you presented and seeing that the conclusions are not a representation of the facts presented, and hopefully someday we'll be speaking from the same page instead of just with the same intentions. Cool

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applesforadam wrote:
I don't doubt that you and the authors are both after truth, the only difference I believe is that any bias I have is based on emperical evidence, whereas yours is purely theistic. However, I also see no benefit in taking a harrassing tone with you since you at least show a willingness toward scientific evidence as opposed to simply saying "well the bible didn't tell me I came from apes so it can't be true." Keep looking, just make sure you are reading between the lines of articles like the one you presented and seeing that the conclusions are not a representation of the facts presented, and hopefully someday we'll be speaking from the same page instead of just with the same intentions. 8-)

Diddo. Thanks for the candid response. It is good to know that just b/c we don't see eye to eye :smt119 doesn't mean we have to be at eachothers throats. :smt117 I know that emoticon doesn't fit into context, but I think some of these are way underused.

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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Pages 26-35 in that article (not summarized) seem to paint a very good case against the mutation/selection model... at least in terms of the Cambrian Explosion, and maybe even beyond.
I'm afraid to summarize it b/c I don't think I am educated enough to do it justice. If anyone has the time to read it... and the patience to bypass a lot of Intelligent Design Parenthesis, I'd love a perspective on it.

Although this article seems to have a lot of really good scientific evidence against mutation/selection, remember this paper is written to disprove what it calls the neo-Darwinistic model and the puctuated equilibrium model, and provide evidence for ID. So be warned. I'm interested in the evidence against mutation/selection.

Call it God. Or come up with another theory extrapolating the logical defintions of nothing and the infinite.


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The Cambrian Explosion and DNA

ha, i agree. i didn't even notice all the extra emoticons, i'll have to make use of them now.


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The Cambrian Explosion and DNA

nacker wrote:
This is gonna be pretty long so I'm going to post it in sections. Here is section I and II.

A Summary of:

The Cambrian Explosion: Biology?s Big Bang
by Stephen C. Meyer, P.A. Nelson, and Paul Chien
by
Nacker

So instead of a 50 page paper, I get nearly an equal length summary. Yah!

Quote:
I. Introduction: Design Without a designer?

The article is introduced by acknowledging that Darwin himself, and neo-Darwinists of our own time ?such as Francisco Ayala, Richard Dawkins and Richard Lewontin,? have acknowledged that biological organisms appear to have been designed by an intelligence, but they will stop at its appearance.

Irrelevent. Darwin, Lewiontin and seval others use design as a rhetorical device, they most assuredly place no stock in it. Quote mining doesn't help one's case.

Quote:
.... The article acknowledges the explanation of natural selection acting on random variations for small scale micro-evolution but begs the question if it can account for the origin of completely new organs, body plans, and structures. This is what the paper wishes to test.

Yet the paper offers no explanation as to why "micro" evolution differs from "macro" evolution. It sets up a strawman from the word go, and the author obviously does not understand exactly what evolution is. What, exactly, is the magical mechanism that prevents "micro" evolution from proceeding to speciation? What say you of the several examples I have posted in this very forum?

Quote:
II The Cambrian Explosion
A detailed definition of the Cambrian explosion that I?ll include only as a paranthesis, assuming that it is understood (sudden appearance in the fossil record of most if not all phyla within 5 million years indicating the presence of a ?complex food web and diverse ecological community?). [see page two for the full explanation]
I found this very interesting:
?The Lower Cambrian sediments near Chengjiang have preserved fossils of such excellent quality that soft tissues and organs, such as eyes, intestines, stomachs, digestive glands, sensory organs, epidermis, bristles, mouths and nerves can be observed in detail. Even fossilized embryos of sponges are present in the Precambrian strata near Chengjiang.10 Cambrian-level strata show the soft body parts of jelly-fish-like organisms (known as Eldonia), such as radiating water canals and nerve rings. These fossils even include the gut contents of several different kinds of animals and undigested food residue in their stools.11? Page 3, 4

So?

Quote:
?The major body plans that arise in the Cambrian period exhibit
considerable morphological isolation from one another (or ?disparity?) and then
subsequent ?stasis.?? 4

Stasis is a relative word, and again, so?

Quote:
?the emergence of the Ediacaran biota (570 million years ago), and then to a much greater extent, the Cambrian explosion (530 million years ago) represent steep climbs up the biological complexity gradient. Indeed, analyzed from an information-theoretic standpoint, the Cambrian explosion in particular represents a remarkable jump in the (specified)18 information content of the biological world.?

An "information-theoretic" standpoint or Behe's and Dembski's "information thoery" are not accepted or scientific proposals.

Oh, and by these dates, we can safely dismiss Biblical creationism, I presume?

Quote:
More complex, multi-cellular organisms would require new cell types which would require specialized proteins, which require more genetic information encoded in DNA.

?For example, molecular biologists have recently estimated that a minimally complex cell would require between 318 to 562 kilobase pairs of DNA to produce the proteins necessary to maintain life.20 Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require an amount of DNA greater by several orders of magnitude (e.g., the genome size of the worm Caenorhabditis elegans is approximately 97 million base pairs21 while that of the fly Drosophila melanogaster (an arthropod), is approximately 120 million base pairs.22 For this reason, transitions from a single cell to colonies of cells to complex animals represent significant (and in principle measurable) increases in complexity and information content.? 5

An increase in "complexity" sure, but I'm seeing nothing here that would prohibit it. The fact of the matter is we KNOW such an evolution happened, via the fossil record this article convieniently cites. That the genetics may not be rock solid in the author's opinion isn't much of a challenge for the over-riding theory of evolution.

What's more, what the author here is citing is the mutation rate amoung NONFUNCTIONAL DNA - stuff that DOES NOT influence evolution. We use the average mutation rate for THIS DNA to gauge time periods precisely because it ISN'T affected by rapid evolution and changes in the environment.

Way to understand the subject you're pontificating on! Laughing out loud

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The Cambrian Explosion and DNA

nacker wrote:
III. Testing the Neo-Darwinian and Punctuated Mechanisms.
.The authors will study the efficacy of neo-Darwinism and punctuated equilibrium as explanations for the Cambrian explosion because:
?(a) neo-Darwinism especially purports to offer a truly creative mechanism of biological change and because (b) the Cambrian fossils attest not only to small-scale variations but also to large scale innovations in basic body plans, the Cambrian data provide a key test of the efficacy of neo-Darwinism?s mutation/selection mechanism.?

No, this isn't a key case. A key case would be organisms which we can actually sequence genetically - such as chimps and humans and the endogenous retrogenes shared between them. Such as the dozens of observed speciation events in recent years (see questions for creationists thread). These are examples of speciation in the observed history of humans, not over the million years history of the Cambrian.

Seriously, we can see evolution happening before our eyes, and they need to go back over 500 MM years to take issue with it Laughing out loud

Quote:
III. A.) Prediction 1: The Gradual Emergence of Biological Complexity and the Existence of Numerous Transitional Forms Leading to Phyla-Level Body Plans

?Given the operation of the neo-Darwinian mechanism, the fossil record should show: (1) the gradual emergence of biological complexity and the existence of numerous transitional forms leading to new phyla-level body plans; (2) small-scale morphological diversity preceding the emergence of large-scale morphological disparity; and (3) a steady increase in the morphological distance between organic forms over time and, consequently, a steady increase in the number of phyla over time.?

Again with the ill defined termed "complexity" - what exactly are we talking about here? Is a worm more complex than a trilobite? If so, how, exactly?

The problem here is that you are looking at single cellular organisms as the basis of this increased "complexity". Any increase in comparison to that base line will appear large.

Let's also not forget that Hox genes, the genes that give bodily mirrorness and body plans first began to develop during this period. This allows for more morphological change for your genomic buck.

There is also absolutely no reason at all evolution should increase the number of phyla present. This is classic ignorance of how evolution works - one species doesn't suddenly become a dozen others, it's not so convieniently simple.

Let's not forget that the majority of phyla, including every plant on the face of the earth, evolved AFTER the Cambrian.

Quote:
As Susumo Ohno has explained:
Assuming a spontaneous mutation rate to be a generous 10-9 per base pair per year and also assuming no negative interference by natural selection, it still takes 10 million years to undergo 1% change in DNA base sequences. It follows that 6-10 million year in the evolutionary time scale is but a blink of an eye. The Cambrian explosion denoting the almost simultaneous emergence of nearly all the extant phyla of the Kingdom Animalia within the time span of 6-10 million years can?t possibly be explained by mutational divergence of individual gene functions.25 page 7

Again, I see no evidence at all here that shows such changes in base pairs did or did not occur, or could or could not accout for the changes observed.

The assumption here also is that mutation rates are constant, and I've already explained why this is incorrect. NONfunctional DNA mutates at a predictable rate, functional DNA does not mutate in any such manner as it is subject to selection. This objection also discounts factors such as punctuated equilibrium. (the earth was coming out of an ice age at the beginning of the Cambrian)

Quote:
?since the variation/selection mechanism involves a trial and error process, both Darwinism (and neo-Darwinism) imply that the fossil record should show many transitional organisms and failed experiments.?

Every extinct species is a "failed" experiment, so there you go, we have millions of such examples. There are also dozens of readily observable "transitional" species in the Cambrian such as transitions between lobopods, antrhopods and worms.

Quote:
?Instead, organisms such as Trilobites (Phylum Arthropoda), with their articulated body plans, intricate nervous systems and compound eyes, first appear fully formed at the beginning of the Cambrian explosion along with many other phyla of equal complexity.? Page 8

Oh, noes, we're missing some fossils, evolution is destroyed :roll:

Evolution does not stand on the fossil record, it would be rock solid without a single fossil from a genetic and morphological and biochemical basis alone.

Quote:
Here the article summarizes punctuated equilibrium and states that the fossil record doesn?t support this theory either, although it was formed to describe the faulty record.

No, Stephen Gould developed the theory of punk eek, and it wasn't invented as an excuse for anything, it arose from Earnst Mayr's work on paripatric vs allopatric speciation.

From what your article says, like there being a rapid evolution and some parts of the fossil record being spotty, I'd say the author is going out of thier way to sump for punctuated equilibria.

Quote:
In light of the Cambrian explosion ?the proposed mechanism of punctuated evolutionary change simply would have lacked the raw material upon which to work.? page 9 Punctuated equilibrium would need a pool of species previous to the explosion which the fossil record does not present.

Again, the theory would require no such thing. ALL punctuated equilibrium says is that speciation is likely to occur at the edges or seperations of a population, and that in such niches survival advantages evolve that can produce a new, non-interbreeding species. A SPARSE population density and a relative LOW number of phyla actually make the process MORE viable.

Quote:
It then summarizes the work of Michael Foote of the University of Chicago on statistical paleontology that supports the work of Valentine and Erwin ?who concluded that ? neither the contending theories of evolutionary change at the species level, phyletic gradualism or punctuated equilibrium, seem applicable to the origin of new body plans? and thus, we now require ?a [new] theory for the evolution of novelty, not diversity.?? page 10.

Wow, an out of context call from a guy who is simply wondering how Hox genes evolved. Score one for you!

Quote:
III. B. III.B. Prediction 2: Diversity Precedes Morphological Disparity (contra
completeness and morphological breadth)

?What are the mechanisms to account for disparity? ?disparity refers to life?s basic themes, whereas diversity refers to the variations on those themes.36? page 10

I hope I do this justice? Obviously evolution does not end at the formation of new species but also accounts in the gradual formation of new genera within one family. ?Later, families will be found to have diverged to the point where taxonomists (specialists in classification) prefer to call them orders, then classes, then phyla?

Taxonomic classification are not hard and fast rules, in fact we SHOULD expect certain populations to be difficult to classify, BECAUSE they are evolving.

Quote:
Ancestors of two different phyla, say vertebrates and molluscs, which we see as built upon utterly different ?fundamental body plans? were once just two species within a genus.? ? Richard Dawkins Page 10, 11.
?Punctuated equilibrium also predicts morphological diversity preceding disparity.?
The fossil record should be a cone pointing down, but looks more like the opposite. In other words, the neo-Darwinian mechanisms responsible for microevolutionary change cannot be extrapolated to explain macro-evolutionary innovation, including the origin of major body plans in the Cambrian period.

This makes no sense at all. Anyone who looks at a phylogenetic tree ought to agree.

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The Cambrian Explosion and DNA

nacker wrote:

More objections coming.

I haven't seen a single legitamet explanation yet, and what's more, I see not alternative scientific explanations to evolutionary theory - exactly what I predicted in my first post in this thread.

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The Cambrian Explosion and DNA

nacker wrote:
IV. OBJECTIONS
IV.A. The Artifact Theory: Is The Cambrian Explosion Real?

Both the author of this piece and I cite the fossil record.

Quote:
?The search for the missing fossils in Precambrian formations all over the world resulted in universal disappointment. Maintaining Darwin?s theory, therefore, eventually required formulating ad hoc hypotheses to account for the absence of ancestral and transitional forms.?

PE is not ad hoc, and even if it were, the objections cited thus far certainly do not challenge it or the TOE in general.

Quote:
The Artifact Theory is summarized: ?the fossil ancestors existed, but for various reasons were not preserved in an ?imperfect and biased?? fossil record. On this theory, the absence of the fossil ancestors represents ?an artifact? of incomplete sampling, a not accurate representation of the history of life. Gaps in the fossil record are apparent, not real.? page 15

Yes, so what? As stated earlier, the theory of evolution does NOT rely on the fossil record, the fossil record is simply extra ammo.

I could easily turn the tables and ask what the lack of evidence literally carved in stone for Christ and God says about Christianity.

Quote:
The article presents many theories that fall under the artifact theory. The ancestors to the Cambrian explosion were too soft to fossilize, or were terrestrial due to tides, or existed as larva. All of these fall short in light of the fossil record. The question of the fossils were too soft was addressed ??animals such as brachiopods and most echinoderms and mollusks cannot exist without a mineralized skeleton. Arthropods bear jointed appendages and likewise require a hard, organic or mineralized outer covering. Therefore the existence of these organisms in the distant past should be recorded either by fossil tracks and trails or remains of skeletons. The observation that such fossils are absent in Precambrian strata proves that these phyla arose in the Cambrian.? page 16, 17

Strawman, already addressed.

Quote:
IV.B. The Ediacaran/Vendian Radiation

These are fossils found all over the world dating from 565 mya to 543 mya. They don?t solve the Cambrian problem however b/c they could only represent 3 to 4 phyla, most have too many morphological dissimilarities with known Cambrian animals, and there is general disagreement on what some are. Even if they should be in the Animal Kingdom.

What Cambrian "problem"? I've yet to see any problem here.

Quote:
Other trace fossils are cited which ?consist of surface tracks and burrows, along with fecal pellets, which, though small, could only have been made by animal organisms of a relatively high degree of differentiation. Thus, some have argued that these trace fossils suggest the existence of organisms with a head and tail, nervous systems, a muscular body wall allowing creeping or burrowing, and a gut with mouth and anus.77 These inferred physical characteristics would indicate organisms of ?organ grade? complexity, above that of flatworms. Much of the discussion about trace fossils is, of course, necessarily speculative. Nevertheless, even on the most optimistic interpretation, these remains suggest the existence of no more than two or so animal body plans (of largely unknown characteristics). Thus, the Ediacaran data taken as a whole hardly establishes the existence of the wide variety of transitional intermediates that neo-Darwinism and punctuated equilibrium require ? page 19, 20

Even with these few phyla, the neo-Darwin and punctuated equilibrium models do not account for the explosion.

The models account for it just fine, and repeating the same "there aren't fossils for every fucking animal that ever crawled the earth" objection doesn't create a problem.

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The Cambrian Explosion and DNA

nacker wrote:

The article says that Intelligent design is not an argument from ignorance.

I'll believe that when I shit rainbow sherbert.

Quote:
It does not claim that just because we don?t know how something is working that we should write it off to design. It claims that ?biological organisms manifest distinctive features, hallmarks or positive indicators of intelligently design systems?that is, organisms possess features that in any other realm of experience would trigger the recognition of prior intelligent activity.?

Ooh, here comes the "irreducible complexity".

Quote:
Subheadings for positive support of ID
V.A. The ?Quantum? Increase in Specified Biological Information

Spinoffs of the failed entropic argument and Behe's and Dembski's information arguments no doubt. Don't bother.

Quote:
V.B. The Persistence of Morphological Isolation or Disparity (Stasis)

How is stasis evidence for ID and NOT punctuated equilibrium?

Quote:
V.C. An Inverted Cone of Diversity: Disparity Preceding Diversity
V.D. Sudden Appearance and Absence of Ancestral Precursors

Yeah, as I already said above, look at the phylogenetic tree.

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The Cambrian Explosion and DNA

What a waste of time.


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The Cambrian Explosion and DNA

Nacker, if you are going to put so much time and effort into studying Anti-Evolution shouldn't you first study evolution?

It is blatantly obvious from your posts that you have devoured massive amounts of anti-evolution propaganda, because you have realised that evolution is one of the biggest threats to your faith.

You say that you wish to discuss these anti-evolution ideas with us, to get both sides of the story. But i have a better idea. If you take the time you spend posting here and actually go read up on ACCEPTED EVOLUTION THEORY, then you get both sides of the story without wasting our time, without wasting your time.