Man-ofGod vs Evolution, etc.

[Man-ofGod]

You see, we actually were able, for what I believe is the first time, to completely test evolution using the scientific method. A question was asked by Darwin, as was a great deal of research. Continuing well after his death, more biologists continued to research, compiling a mountain of evidence and creating a better picture of what that evidence was making clear. the hypothesis that Darwin had once created was now shared by the foremost experts in the world. And now, we've tested this with an experiment and yielded a successful result. After analyzing the results, it becomes clear that not only did a random mutation develop, but that particular mutation was helpful to the organism's survival. And that organism thrived, reproduced creating offspring with the same mutated trait, and that process continued until we could see the clear pattern of evolution.

It was a good day for science. I had cake.

Thanks for sharing the article.

We see that there is an increase in the fitness of the bacteria but not with out a cost.  For example, some lines have lost the ability to repair DNA,  Nature 387 (1997): 703â€"705. However, if you have faith in evolution:

the experiment stands as proof that evolution does not always lead to the best possible outcome.
http://www.newscientist.com/article/dn1 ... e-lab.html
 

But another perspective on this same evidence could make a case for this being an example of adaptation, not evolution.

Molecules-to-man evolution requires an increase in information and functional systems. Instead, these bacteria are likely experiencing a loss of information and functional systems as has been observed in other mutant bacteria in Lenski’s lab. While these changes are beneficial in the lab environment, they do not lead to a net gain that moves bacteria in an upward evolutionary direction.

Lenski’s lab discovered that at generation 31,500, one line of E. coli could utilize citrate (Cit+). As mentioned previously, E. coli are not usually able to utilize citrate (Cit-), and this fact is typically used as diagnostic identification of E. coli. A New Scientist writer proclaims, “A major innovation has unfurled right in front of researchers’ eyes. It’s the first time evolution has been caught in the act of making such a rare and complex new trait.”2 However, as we will see, this is a gross overstatement in regards to what actually occurred.
Previous research has shown that wild-type E. coli can utilize citrate when oxygen levels are low.6 Under these conditions, citrate is taken into the cell and used in a fermentation pathway. The gene (citT) in E. coli is believed to encode a citrate transporter (a protein which transports citrate into the cell).6 When oxygen levels are high, it is thought that the citrate transporter does not function or is not produced (even though they still possess the enzymes necessary to utilize citrate). Thus, wild-type E. coli already have the ability to transport citrate into the cell and utilize itâ€"so much for the idea of a “major innovation” and “evolution . . . making a rare and complex new trait”! Other labs have also produced Cit+ E. coli and speculated that mutation(s) in citT (or its regulators) allow the citrate transporter to function or be produced under high oxygen levels.6, 7 These types of changes are very consistent with the creation model (see below), but cannot serve as a means for evolution.
Lenski’s lab has not yet identified the genetic alterations of the Cit+ E. coli line, but he believes that there are multiple mutations involved. Studies of the “fossil record” of this line indicate that one or more mutations occurred around generation 20,000 which he terms “potentiating” mutations that were necessary before additional mutations around generation 31,500 led to Cit+ cells. Lenski thinks that the mutations may have activated a “cryptic” transporter (a once functional transporter that has been damaged due to the accumulation of mutations) that can now transport citrate. However, he states, “A more likely possibility, in our view, is that an existing transporter has been coopted [sic] for citrate transport under oxic [high oxygen levels] conditions.”1 He believes this could be the same citrate transporter (citT) used in low oxygen conditions (inferring a loss of regulation) or a transporter for another substrate that has been modified to transport citrate (inferring a loss of specificity).
Lenski states (based on calculated mutation rates in E. coli), “It is clearly very difficult for E. coli to evolve this function. In fact, the mutation rate of the ancestral strain from Cit- to Cit+ is immeasurably low . . . .”1 If developing the ability to utilize citrate under certain conditions using random mutations of a pre-existing citrate utilization system is so rare, then how even more improbable is it to believe that these same random mutations can lead to completely new information and functional systems that allow dinosaurs to turn into birds! Lenski’s work shows a clear case of adaptation and not evolution.

[Man-ofGod]

It seems that spirit is squashed, especially when it comes to evolution.

What evidence is there that's against evolution? Other than religion, of course.

I think the real question is, how did it get to theory with out passing the scientific method?

[VanReal]

It seems that spirit is squashed, especially when it comes to evolution.

What evidence is there that's against evolution? Other than religion, of course.

I think the real question is, how did it get to theory with out passing the scientific method?

Please read Will's response on page one, he went through the scientific method for you.

[SSY]

But there is so much evidence. the fossil record shows so many animals in that are slight remakings of the ones before them , leading to clearly defined lineages. Nice attempt at a sidestep though.

The article you cited from nature is nothing to do with this experiment, they concern two, totally different people and experiments. But yes, mutations can help in one way and hurt in others, look at sickle cell anemia for instance.

Also, the refutation of the citrate eating bacteria seems to miss the point entirley. The ones that evolved in the lab can transport citrate at normal oxygen levels, where as un-evolved E.coli cannot. By making a tiny addendum to the technical functioning of the trait, the article claims it is less wonderous, when this is not true at all. A mutation ( or series of mutation ) lead to a change in the way an organism functions, it functions better for a given enviroment, so the mutation is passed on, as subsequent generations can also transport citrate. It says this is somehow consistent with a creator model? What?

The next paragraph is not science at all. Saying the gene loses regulation od specificity is simply erreneous. There is no evidence this is what happened, as the genes have not been mapped yet. The "infer" in the article could more correctly be termed as "guess" or "rationalisation". Even is these things were ture, the way in which they are presented is misleading. By using the word "lose" they try to paint a picture of an organism going backwards, which is simply not true.

Last paragraph is an argument from incredulity, classic logical fallacy.

To address this stuff more generally, Christians love to straw man evolution. They say all mutations lose genetic information ( not true, gene duplication and frame shifting can produce new information, reference to pipebox's excellent post, and also, the multiple types of heamoglobin found in humans ), and that there is some sort of ordering to life. No one organism is "higher" than any other. It is true that one organism cannot evolve into a higher one, becuase there is no such thing as a higher organism. Putting forward a bogus theory, calling it evolution and then debunking it, is not science.

[Will]

But another perspective on this same evidence could make a case for this being an example of adaptation, not evolution.

Mutation is not a part of adaptation. A new trait not only developed, but flourished in it's environment. Is that not the very definition of evolution?

I think the real question is, how did it get to theory with out passing the scientific method?

It has, but I'll get to that in a second. I mention evidence because that's the stage in the scientific method which precedes experimentation. What evidence is there to counter the evidence for evolution? If there is some verifiable evidence, either evolution will need to be changed or replaced with a better theory. If, however, the evidence is not verifiable or scientific, it's not evidence at all.

Regarding the experimentation step of the scientific method being applied to evolution, I may have given you the wrong idea by posting something so recent. Humans have been experimenting with bacteria for many decades now, and as I said above bacteria reproduce very, very quickly and as such evolve at a rate which humans can observe and even experiment with. I've seen studies earlier than the 1950s on bacteria or fruit flies that demonstrate evolution via experimentation. The problem, though, is that once one experiments on evolution, they remove the "natural" from natural selection. We've not only seen, but have been responsible for artificial selection for thousands of years. One could argue that humans first demonstrated evolution of the less natural kind through selective breeding of livestock and crops. We've even caused divergence so great that we've created new species or organism. Natural selection, on the other hand, cannot be experimented on. As soon as one interferes, the process ceases to be natural. It's a paradox, but it doesn't leave us unable to finish.

When I linked the article above, I was providing a part of the puzzle, the patchwork of many, many experiments that eventually created a clear and indeed undeniable picture. Through our many experiments on genetic selection, we've replicated possible real-world situations in which evolution not only can but does take place. Mutation has been experimented on and demonstrated. Selection based on environment has been experimented on and demonstrated. Evolution has passed the scientific method many, many times with flying colors.

Still, that doesn't make evolution gospel. If you have evidence you're holding back, please present it now. It's better to prove something wrong than to believe something that's incorrect.

[Man-ofGod]

Quite the contrary.  The age of the earth was known to be much greater than that derived from biblical studies before Darwin proposed the theory of evolution.

Charles Lyell, you mean the guy who influenced Darwin?  Charles Lyell hypothesized the age of the earth , yes.

And I still find your bringing in of extinction events as a supposed critique of evolutionary theory to be of dubious value.  Geologists are looking at the record of the earth as found in rocks, not as a means of proving or disproving evolutionary theory, but simply to discover what that record says about events in the past.  You seem to think that they are influenced by the current scientific acceptance of the theory of evolution, but in fact all they are doing is reporting on what they've found in the geologic record.  Do you believe that findings that support the biblical story are being suppressed?  If so, please give links to the creationist sites that expose this vast conspiracy.

No. Not at all what I am saying. I am saying that a geologist who has an evolution mindset, will explain an event found in the rocks in the following order,

Does it fit in evolution hypothesis?  lets assume in the example the answer is no.  Well if your a believer, then you overlook that minor defect in your thinking and figure a way to make a fit.


 

Just out of curiosity, since you seem to give it so much importance:  If there seems to be a record of at least five distinct extinction events, separated by layers of strata, how does that equate with one great extinction, caused by a global flood, as recorded in the bible?

The layers of strata is proof in itself of a flood.  On a small scale, what happens when you take for example 5 different types of rocks, put it in a test tube, and shake the test tube? The rocks are sorted into layers of the same type, distributed proportionately by its weight. This is also referred to as Hydraulic sorting. A global flood would obviously have this same effect.  Of course the flood was violent, so its not going to be perfect distribution of weight.  And that fits perfectly w/ what we see in the geological record. For example, the Grand Canyon.

http://www.pbs.org/wgbh/nova/preview/i_3211.html

As for Gentry and the 'polonium halos:'



Thomas Baillieul is not a "layman scientist."

I was thinking of a more J. Richard Wakefield when I said that.

In fact, as I mentioned above, he has a Master's degree in geology, while Gentry is not a geologist, but has a Master's degree in physics.

Gentry doing a geology w/ a master degree in physics is like:

Charles Darwin  observing biology with shaky education in medicine and study of Paley's Natural Theology? or maybe not,  gentry finished his schooling.

Gentry's Doctorate is honorary, and bestowed on him by Columbia Union College, a fundamentalist institution.

And that means what? He earned his Masters degree in physics at the University of Florida, a secular institution.


 

I find the questions and comments about my critique having undergone peer review interesting. My critique is intended to be a peer review of Gentry's polonium halo hypothesis - which itself was never published in its complete form in a mainstream scientific journal nor subjected to peer review. None of Gentry's short papers to Science ever presented the full scope of his study or his conclusions. Most scientific journals do not peer review the comments of their peer reviewers, as those individuals are well known to the journal's editors. In the case of my critique, though, it was reviewed extensively prior to posting.

The original manuscript was submitted for publication in the Records of the National Center for Science Education. The paper was reviewed by the journal's editor, Andrew Petto (senior lecturer in anatomy and physiology at the University of Wisconsin), and Lorence Collins (Emeritus Professor of Geology at California State University Northridge). An additional scientist with nuclear radiation background also reviewed the manuscript for the journal, although I was never given his name (science journals seldom identify their reviewers to the prospective authors for a variety of reasons; Collins self-identified himself to me). All reviewers agreed with my arguments and felt the work warranted publication. However, they felt that the material was too technically complex and lengthy for the average readership of the Records of the NCSE Looking to present the critique to the widest audience possible, I chose instead to submit the revised paper to the Talk Origins Archive. Prior to posting, there was additional technical and editorial review by Talk Origins' coordinators. Following initial posting on the Talk Origins page, I received technical comments from a specialist in radiation effects on biological materials, leading to an expansion of my discourse on the Bragg Effect in minerals. I also had extensive correspondence with 2 creationists which resulted in expanding and clarifying several sections of the paper to make the arguments clearer to a lay audience.


At the end of his 1974 paper in Science, Gentry asks the question about polonium halos: "...can they be explained by presently accepted cosmological and geological concepts relating to the origin and development of the Earth?" I believe my critique answers that question in the affirmative as well as showing Gentry's work to be flawed and incomplete.

 

Gentry's polonium halo hypothesis for a young Earth fails, or is inconclusive for, all tests. Gentry's entire thesis is built on a compounded set of assumptions. He is unable to demonstrate that concentric haloes in mica are caused uniquely by alpha particles resulting from the decay of polonium isotopes. His samples are not from "primordial" pieces of the Earth's original crust, but from rocks which have been extensively reworked. Finally, his hypothesis cannot accommodate the many alternative lines of evidence that demonstrate a great age for the Earth. Gentry rationalizes any evidence which contradicts his hypothesis by proposing three "singularities" - one time divine interventions - over the past 6000 years. Of course, supernatural events and processes fall outside the realm of scientific investigations to address. As with the idea of variable radioactive decay rates, once Gentry moves beyond the realm of physical laws, his arguments fail to have any scientific usefulness. If divine action is necessary to fit the halo hypothesis into some consistent model of Earth history, why waste all that time trying to argue about the origins of the haloes based on current scientific theory? This is where most Creationist arguments break down when they try to adopt the language and trappings of science. Trying to prove a religious premise is itself an act of faith, not science.

In the end, Gentry's young Earth proposal, based on years of measuring discoloration haloes, is nothing more than a high-tech version of the Creationist "Omphalos" argument. This is the late nineteenth century proposition that while God created the Earth just 6,000 years ago according to the Genesis account, He made everything appear old. Unfortunately, because Gentry has published his original work on haloes in reputable scientific journals, a number of basic geology and mineralogy text books still state that microscopic discoloration haloes in mica are the result of polonium decay.

Your link is basically just a blog w/ out the comments.  Thomas states that he is disputing scientific work that gentry did not publish in scientific journals, but then goes on to write a whole article on the very work gentry published in scientific journals?  It is obvious Thomas work will not gain acceptance into any scientific journal.  His writing is just propaganda.

God did it!

Sounds similar to  "evolution did it!"

[Man-ofGod]

Please read Will's response on page one, he went through the scientific method for you.

You mean this

You see, we actually were able, for what I believe is the first time, to completely test evolution using the scientific method

.

Two things, this would imply that evolution was not a theory before this study.  The second is that this study on page 1 does not explain evolution, especially when looked in the light of how bacteria evolved to current day humans. Which is the only evolution I care about.  Which is still scientifically, unproven, therefore a belief.

[Will]

Two things, this would imply that evolution was not a theory before this study.

This assumes that the article I linked was the first experiment to demonstrate evolution.

The second is that this study on page 1 does not explain evolution, especially when looked in the light of how bacteria evolved to current day humans. Which is the only evolution I care about.  Which is still scientifically, unproven, therefore a belief.

You imply disparity where none exists. There's no difference between bacteria developing the ability to utilize a particular citrate and bacteria over billions of years evolving into humans or a tree or even a Republican.

Maybe that's where Creationists get confused. Maybe they can't really conceptualize the scope of time involved in evolution. If in the span of a few decades bacteria can develop a whole new way to utilize a citrate, imagine what could happen in 100 years, the amount of time from the first airplane to a mach ten X43 airplane. Now imagine what could happen in 500 years, the time from the first Europeans finding the Americas to now. Now imagine what could happen in 1000 years, the amount of time that's passed since the dawn of the Middle Ages. Now imagine what could happen in 10,000 years, the time between now and the dawn of human civilization. If that mutation could happen in a few decades, how much has happened since the dawn of human civilziation? Now multiply that by at least 350,000. The oldest fossils of microscopic life dates back 3.5 billion years, but there's evidence that suggests that life started closer to 4.7 billion years old, plus or minus a few hundred million years. You can't understand evolution without comprehending the scope of time that life has been evolving.

[PipeBox]

The layers of strata is proof in itself of a flood.  On a small scale, what happens when you take for example 5 different types of rocks, put it in a test tube, and shake the test tube? The rocks are sorted into layers of the same type, distributed proportionately by its weight. This is also referred to as Hydraulic sorting. A global flood would obviously have this same effect.  Of course the flood was violent, so its not going to be perfect distribution of weight.  And that fits perfectly w/ what we see in the geological record. For example, the Grand Canyon.

OK, no, just no.  I'm not a geologist but I can tell you the difference between stratification and hydraulic sorting.  Courtesy of the video at the end of the post, which will do a far better job (and it is one of many).  BUT!  Far better is that the stratification that we see is often heavier sediments on top of lighter ones.  Soil on top of pumice on top of redstone on top of sandstone on top granite on top of basalt.  If the heavier, more dense stuff is on top, the this hydraulic sorting fails to explain it.  

... how bacteria evolved to current day humans. Which is the only evolution I care about. Which is still scientifically, unproven, therefore a belief.

OK, first off, bacteria popularly belong to domain prokaryota (I say popularly because they actually belong to domain bacteria but they are prokaryotes along with domain archaea), while we're eukaryotes, like the protists.  The domains are the largest taxonomic structures describing the most basic features shared by all life, aside from being protein based and possessing RNA, which fits both groups in a clade sometimes called gaia biota, describing all life on this planet.  But that's seldom used.  So we share a commonality with all other eukaryotes, and reasonably a common ancestor, as it is an undisputed fact that all of our cells are initially nucleic.  If you're saying we haven't observed protists evolving into animals and all the way up to hominids, well, no kidding.  We've also never seen Sedna orbit the sun, but it sure looks like it does!  We've never, in our recorded history, completed a galactic transit, even more so if you believe the Earth to be 6000 years old and the Milky Way, too (nevermind the galaxy is 100,000 ly across, so we shouldn't even be able to see it unless God wants to trick us into thinking the universe is very old)!  Should we assume that these aren't proven to happen just because we've only seen minor pieces of the orbits we think have happened in the past?  Not at all!  In this case, we know what we've observing, we know it's part of an ongoing process, and through induction (and I use that word lightly, as it doesn't require much induction to figure out) we know how it came to be where it is.  I can't impress on you how much evidence there is in biology that we share a common ancestor.  Please, ask whatever you like, but do ask!


But here's that video:

[youtube:e6vftaek]http://www.youtube.com/watch?v=_sD_7rxYoZY[/youtube:e6vftaek]

[Recusant]

Charles Lyell, you mean the guy who influenced Darwin? Charles Lyell hypothesized the age of the earth , yes.

Yes.  Geology is a different branch of science than biology.  It deals with rocks and land formations, and seeks to understand what the evidence found in it's field of study tells us.  That evidence led Hutton and Lyell to think that the age of the earth was much greater than that which biblically influenced ideas current in their time gave.  In other words, they, and the geologists who followed, were not intent on proving the theory of evolution at all, in fact it did not even exist when they began to propose a greater age for the planet than had previously been supposed.  Geology since their time has revised and built upon their ideas, as more evidence has been gathered, and that evidence has been understood more comprehensively. Geologists have a geology mindset, not an 'evolutionist mindset.'  They report what they find.  Those findings have backed up the theory of evolution, but that is not their intent at all. Basically you are accusing the whole science of geology of being intellectually dishonest, of looking only to find what backs up a theory that is not even part of their field, and ignoring evidence to the contrary:

 

I am saying that a geologist who has an evolution mindset, will explain an event found in the rocks in the following order,

Does it fit in evolution hypothesis? lets assume in the example the answer is no. Well if your a believer, then you overlook that minor defect in your thinking and figure a way to make a fit.

Please give an example of geological evidence fitting  your description.  Evidence which shows the earth to be much younger than currently understood by the science of geology, and which has therefore been either ignored or explained away in an intellectually dishonest manner.  And please don't bring  Dr. Gentry into this particular portion of the debate since his book is in dispute elsewhere.  If there's  such a preponderance of evidence for the creationist view that it's convinced you of it's truth, then it shouldn't be hard to find another example.

 

The layers of strata is proof in itself of a flood. On a small scale, what happens when you take for example 5 different types of rocks, put it in a test tube, and shake the test tube? The rocks are sorted into layers of the same type, distributed proportionately by its weight. This is also referred to as Hydraulic sorting. A global flood would obviously have this same effect. Of course the flood was violent, so its not going to be perfect distribution of weight. And that fits perfectly w/ what we see in the geological record. For example, the Grand Canyon.

I see this has been answered above, but I have a few questions none the less:  Why would different groupings of fauna be buried in separate layers, so that the evidence would seem to show that at one time the ecology of the planet was different than the grouping of fauna found several layers above it would indicate?  If there was only one catastrophic flood, one would imagine that all of the animals killed in that flood would be  in one huge layer, and that layer would only indicate one dead ecology.  Why would different types of animals be found in different layers? Why do multiple layers indicating multiple (quite distinct) ecologies exist?

 

And that means what? He [Gentry] earned his Masters degree in physics at the University of Florida, a secular institution.

I was merely indicating that when one reads Dr. Gentry, one should not be mislead into thinking that he has a higher level of academic qualification than Thomas Baillieul.

 

Your link is basically just a blog w/ out the comments. Thomas states that he is disputing scientific work that gentry did not publish in scientific journals, but then goes on to write a whole article on the very work gentry published in scientific journals? It is obvious Thomas work will not gain acceptance into any scientific journal. His writing is just propaganda.

Actually, if you read the Baillieul article, you will see that he is addressing Gentry's theory in general, including the book Creation's Tiny Mystery. which as you well know was not published in scientific journals. If you find Baillieul's article unacceptable, since it was admittedly not published by a scientific journal, perhaps you might care to read The Geology of Gentry's "Tiny Mystery", which was originally published in the May 1988 Issue of the Journal of Geological Education.  This article takes a slightly different approach in critiquing Gentry's work, but comes to much the same conclusion as Baillieul.

I would like you to address just one sentence from the Baillieul article, however:

 

If divine action is necessary to fit the halo hypothesis into some consistent model of Earth history, why waste all that time trying to argue about the origins of the haloes based on current scientific theory?

Thank you, Man-ofGod, for your willingness to examine these issues with us, and for your continued well-mannered approach to this debate.  I admire that.

[karadan]

Maybe that's where Creationists get confused. Maybe they can't really conceptualize the scope of time involved in evolution. If in the span of a few decades bacteria can develop a whole new way to utilize a citrate, imagine what could happen in 100 years, the amount of time from the first airplane to a mach ten X43 airplane. Now imagine what could happen in 500 years, the time from the first Europeans finding the Americas to now. Now imagine what could happen in 1000 years, the amount of time that's passed since the dawn of the Middle Ages. Now imagine what could happen in 10,000 years, the time between now and the dawn of human civilization. If that mutation could happen in a few decades, how much has happened since the dawn of human civilziation? Now multiply that by at least 350,000. The oldest fossils of microscopic life dates back 3.5 billion years, but there's evidence that suggests that life started closer to 4.7 billion years old, plus or minus a few hundred million years. You can't understand evolution without comprehending the scope of time that life has been evolving.

You just hit the nail on the head.
 

[Man-ofGod]

But there is so much evidence. the fossil record shows so many animals in that are slight remakings of the ones before them , leading to clearly defined lineages. Nice attempt at a sidestep though.

I think this is more of a case of side stepping the scientific method, a pillar of science. This is the same wolf and the dog argument. One argument states these are two different species and proof of evolution, the other side states its the same kind of animal and proof of Creation (“Let the earth bring forth the living creature according to its kind" - Genesis 1:24). Which side is correct? From a science point of view, neither is correct or incorrect , both fit.

The article you cited from nature is nothing to do with this experiment, they concern two, totally different people and experiments. But yes, mutations can help in one way and hurt in others, look at sickle cell anemia for instance.

No argument from me there.  edit** did not see your nature post.. I will address when I get back to thread.

[Sophus]

"I think this is more of a case of side stepping the scientific method, a pillar of science," said the Man of God. lol. I'm sorry am I the only one who finds that funny?  

[curiosityandthecat]

"I think this is more of a case of side stepping the scientific method, a pillar of science," said the Man of God. lol. I'm sorry am I the only one who finds that funny?  

[rlrose328]