Myth of evolution and new drug discovery

[StAnastasia]

Hey StA, would you consider posting the transcript of you public lecture? Or will it remain private?

I’m not sure how to do it – it’s not a written text but sixty PowerPoint slides. We covered a lot of ground, from the philosophy of science to biblical interpretation, theological anthropology, soteriology, theodicy, and eschatology. It was for a Catholic high school – sort of a capstone course for senior women. We discussed six areas of Catholic doctrine in light of evolution.

 

[StAnastasia]

Hang in there – keep the Darwinian faith and don’t get discouraged! Your atheism will see you through - with pseudo-Catholics to help you avoid being converted.

Reggie, I don’t have faith in Darwin, but I do have faith in God.

 

[pzona]

reggieM,
I understand exactly what you’re saying. Many atheists do have a vendetta against religion, and many scientists are atheists. However, many atheists seek only to understand religion. I like to think that I’m pretty impartial (most of the time anyway) as far as religion goes. When you say that most scientists are atheists, therefore most scientists have a vendetta against religion, you’re doing the same thing as the people who classify all Christians as fundamental extremists. Science can be compared to the church in some ways. It is a field dominated by people who try to disprove the existence of God rather than trying to objectively decide whether or not God exists. It is an imperfect organization run by imperfect people. True science is about truth. I am an atheist, but if there were evidence (physical evidence, not anecdotal “miracle” stories) that pointed toward God, I would be forced to reconsider my views. I believe in that which I know to be real, and currently that does not include God. I understand the faith argument, but I’m a science oriented person, and I cannot believe in something based on faith alone. I maintain that a lot of the tension between science and religion is based on misunderstanding, and the fact that people often refuse to use objective judgment when deciding what is truth and what is not.

 

[SonofMonica]

reggieM,
I understand exactly what you’re saying. Many atheists do have a vendetta against religion, and many scientists are atheists. However, many atheists seek only to understand religion. I like to think that I’m pretty impartial (most of the time anyway) as far as religion goes. When you say that most scientists are atheists, therefore most scientists have a vendetta against religion, you’re doing the same thing as the people who classify all Christians as fundamental extremists. Science can be compared to the church in some ways. It is a field dominated by people who try to disprove the existence of God rather than trying to objectively decide whether or not God exists. It is an imperfect organization run by imperfect people. True science is about truth. I am an atheist, but if there were evidence (physical evidence, not anecdotal “miracle” stories) that pointed toward God, I would be forced to reconsider my views. I believe in that which I know to be real, and currently that does not include God. I understand the faith argument, but I’m a science oriented person, and I cannot believe in something based on faith alone. I maintain that a lot of the tension between science and religion is based on misunderstanding, and the fact that people often refuse to use objective judgment when deciding what is truth and what is not.

Some folks do not possess the innate ability to simply have faith, so there’s no need to apologize, I assure you. Some folks are brought around to adhere to religion, among other ways, by its ordered implementation and/or subjective applicability to their respective personal situations; and yes, through anecdotes, not just other people’s stories, but personally experienced “miracles.” Some experience great peace, order and centeredness when they actually put the religion to practice. The truth is revealed to them through implementation, and the objections fade away not because of logical progression from revelation, but because of experience; an experienced difference. I know, because I am one of them.

So in light of what I’ve just said, I’ll share a tiny bit with you. My wife and I both separately came to the conclusion that our usage of artificial birth control was driving us apart and destroying our young and fledgling marriage. But we didn’t arrive at that conclusion because the Church told us it would drive us apart or destroy anything or because the Church labeled it evil. Rather, this is an example of a previously held objection to God and his Church’s morality fading away because of personal experience. We both had the thought, maybe there’s some truth to birth control’s evil, not simply because the Catholic Church is telling us there is; maybe the truth exists out there and we have just experienced the “evil” at work in our marriage. It did not do anything but destroy our sexual relationship. In fixing the problem on a practical level, our previous objection to the Church’s stance on birth control became moot through practical experience. I can tell you this experience is only a fraction of what is bringing us (out of atheism for me) into the Church.

The Bible is filled with stories, not just of God and men saying “I am the Truth” “This is the truth,” but also of regular people exclaiming “Look what God did for me!” I wouldn’t expect you to believe in God because of what’s happened in my life; I would expect you to feel at liberty to attempt to explain it away, or at least insist there must be a natural explanation. You are free to call me delusional or prone to superstition. Like most Christians, my only choice in a world of skepticism (whether rightly or wrongly held) is to do my best to live it out, and if you are looking for God, maybe you will find Him the exact same way–through trying Him. I just ask you to think about this: do not be so quick to discount personal experience. You may find it’s all we really have, or at least all that really counts for much.

 

[StAnastasia]

Science can be compared to the church in some ways. It is a field dominated by people who try to disprove the existence of God rather than trying to objectively decide whether or not God exists… I believe in that which I know to be real, and currently that does not include God. I understand the faith argument, but I’m a science oriented person, and I cannot believe in something based on faith alone. .

pzona, this is thoughtfully put. However, I don’t agree with you that science “is a field dominated by people who try to disprove the existence of God.” In my experience science 's a field of people researching the way nature works. Some of them are atheists, some don’t know what to think about God, and some say Mass before the go to teach or work in the lab.

Also, I too believe in that which I know to be real. I know too many people for whom God is real to doubt their (and my own) experience. I have faith that what we collectively experience is truly of God.

StAnastasia

 

[reggieM]

The figure for ‘Recent’ is too large because we do not have any fossils for most of those phyla - the animals are all small squishy marine worms and similar with no hard parts.

This is the claim that the fossil record is “imperfect” – which was refuted in the original article posted in this discussion. Beyond that, with the whole world of evolutionary biology and paleontology for support, this is all that they can come up with.

As for the suddenness of the appearance of the fossils, we could try more credible sources than the Encyclopedia article I found quickly :

Fossils, molecules and embryos: new perspectives on the Cambrian explosion.Valentine JW, Jablonski D, Erwin DH. Collaborators (1) Erwin DH.
Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, CA 94720, USA. jwv@ucmp1.berkeley.edu

The Cambrian explosion is named for **the geologically sudden appearance **of numerous metazoan body plans (many of living phyla) between about 530 and 520 million years ago, only 1.7% of the duration of the fossil record of animals. Earlier indications of metazoans are found in the Neoproterozic; minute trails suggesting bilaterian activity date from about 600 million years ago. Larger and more elaborate fossil burrows appear near 543 million years ago, the beginning of the Cambrian Period … All living phyla may have originated by the end of the explosion.

The cambrian evolutionary explosion recalibrated
Richard A. Fortey 1, Derek E. G. Briggs 2, Matthew A. Wills 2
1Department of Paleontology, Natural History Museum, Cromwell Rd, London SW7 5BD, UK
2Department of Geology, University of Bristol, Queens Street, Bristol B58, UK

**The sudden appearance in the fossil record **of the major animal phyla apparently records a phase of unparalleled, rapid evolution at the base of the Cambrian period, 545 Myr ago. This has become known as the Cambrian evolutionary explosion, and has fuelled speculation about unique evolutionary processes operating at that time.

Early evolution of animal cell signaling and adhesion genes
Scott A. Nichols*, William Dirks†, John S. Pearse‡, and Nicole King
University of California, Berkeley, CA, and approved June 28, 2006

The fossil record from ≈540 Mya documents **the abrupt appearance of fully diversified eumetazoan body plans **during the “Cambrian explosion.” In contrast, fossil evidence of sponges dates to ≈580 Mya and reveals that **their simple body plan predates the Cambrian and has since remained relatively unchanged **(1, 2).

Towards a new evolutionary synthesis
Robert L. Carroll
Robert Carroll is at the Dept of Biology and is Curator of Vertebrate Paleontology, Redpath Museum,
McGill University, 859 Sherbrooke St. West, Montreal, PQ, Canada H3A 2K6
(robertc@shared1.lan.mcgill.ca).
The most conspicuous event in metazoan
evolution was **the dramatic origin of
major new structures **and body plans documented
by the Cambrian explosion10,11.
Until 530 million years ago, multicellular
animals consisted primarily of simple,
soft-bodied forms, most of which have
been identified from the fossil record as
cnidarians and sponges. Then, within less
then 10 million years, almost all of the
advanced phyla appeared, including
echinoderms, chordates, annelids, brachiopods,
molluscs and a host of arthropods.
The extreme speed of anatomical
change and adaptive radiation during this
brief time period requires explanations
that go beyond those proposed for the evolution
of species within the modern biota.

 

[StAnastasia]

Like most Christians, my only choice in a world of skepticism (whether rightly or wrongly held) is to do my best to live it out, and if you are looking for God, maybe you will find Him the exact same way–through trying Him. I just ask you to think about this: do not be so quick to discount personal experience. You may find it’s all we really have, or at least all that really counts for much.

SonofMonica, I think you are quite right. In the end all we have is our experience – of the liturgy, the scriptures, the life of the Church, our moral lives, the lives of the saints, and the many little miracles that make up religious experience. We may choose to view all of these through the lens of theism or through the lens of atheism.

StAnastasia

 

[StAnastasia]

This is the claim that the fossil record is “imperfect” – which was refuted in the original article posted in this discussion. Beyond that, with the whole world of evolutionary biology and paleontology for support, this is all that they can come up with…Then, within lessthen 10 million years, almost all of the advanced phyla appeared, including echinoderms, chordates, annelids, brachiopods, molluscs and a host of arthropods. The extreme speed of anatomical change and adaptive radiation during this brief time period requires explanations that go beyond those proposed for the evolution of species within the modern biota.[/INDENT]

Yes, isn’t that marvelous? Science is progressive in nature.

 

[SonofMonica]

Yes, isn’t that marvelous? Science is progressive in nature.

I would say that true science is progressive in nature, and it stems from humility. Unfortunately, much of what passes for scientific thought this days is mere parroted skepticism.

As G.K. Chesterton noted, more eloquently than I could put it, “Latter-day scepticism is fond of calling itself progressive; but scepticism is really reactionary. Scepticism goes back; it attempts to unsettle what has already been settled. Instead of trying to break up new fields with its plough, it simply tries to break up the plough.”

He also had a couple more interesting quotes about progress that should make us think…

“Progress is a comparative of which we have not settled the superlative.”

“Progress should mean that we are always changing the world to fit the vision, instead we are always changing the vision.”

 

[StAnastasia]

I would say that true science is progressive in nature, and it stems from humility. Unfortunately, much of what passes for scientific thought this days is mere parroted skepticism. As G.K. Chesterton noted, more eloquently than I could put it, “Latter-day scepticism is fond of calling itself progressive; but scepticism is really reactionary. …”

Yes, I agree; I meant “progressive” in the literal sense that science builds upon past knowledge. I did not mean it in sense of the claim that people in 2009 have “progressed” to a higher state of morality, or a better culture. I do think it’s a good thing that we don’t burn people at the stake like they did 400 years ago, although of course, that advance is canceled out by the skyrocketing abortion rate today.

The progressive character of scientific knowledge is reflected in the fact that we now ascribe earthquakes to plate tectonics, not to the earth farting. We now recognize genetic lineages and divergencies, and ascribe that to evolution. We now ascribe the falling of apples and planetary orbits to gravity rather than to Aristotelian “natural place.” We have progressed in our knowledge.

 

[rossum]

This is the claim that the fossil record is “imperfect” – which was refuted in the original article posted in this discussion.

You really need to think what you are saying through to its conclusion. I said that the fossil record was imperfect, so we could not determine when a number of small squishy marine phyla originated because we have no fossils of them though we do have living examples. If you maintain that the fossil record is perfect, then we still have no fossils of those phyla and must conclude that they all originated recently, long long after the Cambrian.

The imperfection of the fossil record helps your argument for the importance of the Cambrian explosion, not hinders it. If the fossil record is imperfect then I can agree that many of those ‘Recent’ phyla did in fact originate in the Cambrian, it is just that we do not have fossils because they do not fossilise well. If you say that the fossil record is perfect then I can no longer agree - if they were that old then we would have the fossils to show it.

You also fail to observe that many of your sources are talking about animal phyla only. Some even restrict that to ‘major’ animal phyla. Everybody agrees that plant phyla originated long after the Cambrian. Anyone who claims that “all” phyla originated in the Cambrian is wrong. Many major animal phyla did originate in the Cambrian. Some, such as sponges, originated before and others, such as Bryozoa, originated afterwards. Some we do not have a date for.

rossum

 

[buffalo]

Yes, isn’t that marvelous? Science is progressive in nature.

Here we have Revelation - given by God solid lasting truth.

Here we have science - done by humans trudging along, theorizing, correcting, biasing, imagining, observing.

Will science ever match up or catch up to the truths of the Bible?

 

[hecd2]

Thanks for the note. I just finished a book by Francisco Ayala. I was impressed with his clear reasoning and especially his attitude about the subject.

Yes, I recommend the book he wrote with Camilo Jose Cela-Conde. Human Evolution, Traols from the Past published by Oxford University Press in 2007, which is an insightful and quite up to date review of the subject.

I’m busy now trying to take in what I can regarding recent interpretations of the fossil record. As far as the current issue is concerned here on CAF regarding what you said genetics research discloses, I have to study up more on that so I won’t be proffering opinions without supporting evidence. Opinions without good supporting evidence aren’t worth anyone’s time.

Chapeau!

And those other “important factors” I alluded to…I do not think, after all, I can articulate them with sufficient clarity at this time. Hence, it will be awhile before I say anything much on this topic. I have some homework to do on the subject first. That includes reviewing your posts. I appreciate the information you provided.

Well, I would be interested in seeing what you come up with if and when you feel able to articulate it.

Alec
evolutionpages.com

 

[hecd2]

Addendum to my initial reply to this post: I thought I would just add how I propose to “resolve” the discrepancy under discussion. I am tending to consider a bottleneck as highly improbable but not absolutely impossible. Furthermore, from a bottleneck in human history an effective population can be attained in a small number of generations. The issue of a bottleneck is one where I must invoke what I consider to be a healthy skepticism, one that takes into account the fact “solid” conclusions in science may be subject to revision or modification when warranted by the implications of previously unknown facts.

I offer this comment without argument merely as an indication of my current state of mind. However, feel free to respond to or object to anything I have said here in any way you see fit. Nonetheless, I am not, as I previously indicated, sufficiently knowledgeable or prepared to discuss this matter in detail at this time.

Well, I respect the fact that you don’t feel ready to discuss in detail, so will offer a couple of comments, also without argument so that you can mull over them while developing your position.

I am struck by the similarity between your current state of mind (a bottleneck of two is improbable but not impossible; the possible rapid growth of a much larger effective population from two, and the tentative nature of scientific conclusions as warrants for maintaining a belief in literal Adam and Eve) and the detailed arguments put forward by Dennis Bonnette in discussion with me. Let me just say:

a) that a bottleneck of two is arithmetically precluded by the number of alleleic lineages at some loci carried througout human evolution which exceeds that which can originate with two individuals

b) other aspects of the human genome lack the essential signature of an extreme bottleneck such as reduced polymorphism and heterozygosity, and an overabundance of common deleterious alleles

c) Achieving mean effective population sizes, Ne, of 10,000 during the Pleistocene which numerous studies of molecular diversity support, whilst at some time passing through a bottleneck of two, demands unobservable and untenable population growth rates over 10 - 20 generations, because mean effective population is the harmonic mean of population in the relevant generations

d) such rapid growth would lead to a signature on the genome (an overabundance of rare alleles) that we do not see

e) scientific conclusions are never “proofs” but our confidence in the conclusion depends on the strength of the evidence. One can justify any belief that conflicts with a scientific conclusion by playing the “tentative nature of science” card but there comes a point when the evidence is such that to do so requires a rather eccentric epistemology. Of course, if you are aware of specific findings that call for a revision of the conclusion, then this objection takes on a different aspect.

I don’t expect a reply unless and until you have read up on the subject and feel ready to put forward a detailed case (although of course I welcome any reply you make at any time).

Alec
evolutionpages.com

 

[StAnastasia]

Here we have Revelation - given by God solid lasting truth. Here we have science - done by humans trudging along, theorizing, correcting, biasing, imagining, observing. Will science ever match up or catch up to the truths of the Bible?

Buffalo, I may have lunch today with the devil’s chaplain. Anything you want me to communicate to Richard Dawkins him from you if I see him? That is, assuming he’s civil to me as a Roman Catholic. I promised the group I’d put away my vestments, extinguish the incense, and turn down the Gregorian chant…

 

[buffalo]

Buffalo, I may have lunch today with the devil’s chaplain. Anything you want me to communicate to Richard Dawkins him from you if I see him? That is, assuming he’s civil to me as a Roman Catholic. I promised the group I’d put away my vestments, extinguish the incense, and turn down the Gregorian chant…

You could invite him to participate in CAF. Maybe we could start a new forum called StA and Cohorts. You could post your papers and transcripts of your presentations to undergo Catholic peer review. (if you dare)

 

[hecd2]

“science is about truth”? Birds evolved from dinosaurs? That was true until a few weeks ago.

Whilst the claim you are responding to is that the objective of science is to seek truth about the way nature works, not that every scientific claim is true (do you understand the difference?), you show your contempt for truth by deliberately misrepresenting things (even after you’ve been corrected).

The proposition that birds evolved from dinosaurs has been *strengthened *not weakened in the last few weeks (Hu et al, A pre-Archaeopteryx troodontid theropod from China with long feathers on the metatarsus, *Nature *461, 640 - 643), and is more likely to be true than ever. Your statement is therefore false and misleading.

On Sep 30th I said this on post 71 of this thread about this very claim last time you made it when I also pointed out that it is wrong: “Ed is doing what he commonly does, which is selective quoting and deliberate misrepresentation. I bet that he doesn’t acknowledge his mistake and that he continues to claim that it’s been proven that birds did not evolve from dinosaurs in spite of the fact that that’s plain false.” You’ve taken barely a week to prove me right.

Junk DNA? It’s turning out that the non-coding, assumed ancestral, trial and error, left over stuff from millions of years of evolution is not junk, but it was ‘true’ for a while based on a preconceived idea.

Although the importance of some regulatory and promotional non-coding sequences is greater than was once recognised, the non-functionality (ie junkiness) of the non-coding DNA is still proposed for the *vast *majority of non-coding LINES, SINES, Alus, retrotransposons, tandem repeats, pseudogenes etc that make up the bulk of the mammalian genome, and of course its ancestral origin in retroviruses, broken genes, duplications and translocations etc stands whether it is functional or not. Your claim is another another misrepresentation of the science. (By the way, what is the preconceived idea rather than the evidence and reasoning that led scientists to think that all non-coding DNA sequence was non-functional? And do you recognise that you wouldn’t know the difference between DNA and a Mexican hat, never mind what a coding and non-coding sequence is, if it wasn’'t for those guys with the “preconceived ideas”).

(By the way, I wouldn’t use the argument that functionality of some non-coding DNA shows that the genome is intelligently designed if I were you - the more function that is found for these sequences, the more it demonstrates the ability of evolution to incorporate and find uses for various bits of DNA that randomly turn up in the genome from retroviral insertions and from random sequence duplications. They are completely *not *what one would expect in the case of design).

Alec
evolutionpages.com

 

[StAnastasia]

You could invite him to participate in CAF. Maybe we could start a new forum called StA and Cohorts. You could post your papers and transcripts of your presentations to undergo Catholic peer review. (if you dare)

I’m not sure what you mean by "cohorts, but it would include priests, bishops, and several hundred Catholic theologian colleagues. The discussion would be lively and theologically informed , and would probably fill threads up to the thousand post limit fairly fast. But we could try.

StAnastasia

 

[buffalo]

I’m not sure what you mean by "cohorts, but it would include priests, bishops, and several hundred Catholic theologian colleagues. The discussion would be lively and theologically informed , and would probably fill threads up to the thousand post limit fairly fast. But we could try.

StAnastasia

You are not putting up obstacles now are you? I think it would be well worth it.

Start simply. Invite your cohorts to share with us their wisdom.

 

[StAnastasia]

Here we have Revelation - given by God solid lasting truth. Here we have science - done by humans trudging along, theorizing, correcting, biasing, imagining, observing. Will science ever match up or catch up to the truths of the Bible?

Buffalo, you are right that the Bible gives solid and lasting truth. However, that does not mean that human perceptions of God don’t evolve over time. The Jesus portrayed in the New Testament is a far different character than the God portrayed in the Old Testament. In Richard Dawkins’ characterization,

“The God of the Old Testament is arguably the most unpleasant character in all fiction: jealous and proud of it; a petty, unjust, unforgiving control-freak; a vindictive, bloodthirsty ethnic cleanser; a misogynistic, homophobic, racist, infanticidal, genocidal, filicidal, pestilential, megalomaniacal, sadomasochistic, capriciously malevolent bully.”

Now, it should be observed that while there is some truth to what he says, Dawkins is egregiously selective in what it is in the Bible to which he refers (sacrifice, wars, unjust executions, mass drownings, murders of innocent babies, etc.). He misses out on perceiving the passages representative of divine mercy, tenderness, and love.

StAnastasia