Is ID non-scientific because it has relgious implications?

[frankbaginski]

ARWallace,

Thank you for your thoughful response. I am sorry that I assumed some things from your post. Evidently I put two and two together and came up with seven. I will try and be more careful in the future.

I think we are getting somewhere in this dicussion. I would suggest that we keep the discussion somewhat at a higher level and not get too washed in detail. I think this discussion is being read by people with a wide range of backgrounds and if we keep the post at a description level it would help me and possibly others. I am familiar with the basic mechanics in molecular biology, it seems you are way more knowledgeable about a wide variety of species than I am. The flagellum and a few others are the only structures I have studied so this example would be great.

To get from one species to another requires some massive (number of neucleotides) changes in DNA and support structure. Now I know that many mechanisms have been identified which may allow a transfer of information from one cell into another. This can be injected, it can come from flipped parts of DNA, and can just be duplicated. These mechanisms can explain some of what we see in DNA and I will not argue against these paths of transfer of data. So from my perspective there are two evolutionary mechanisms that could produce new species, one being mutations and the other being a transfer of data. Now I don't feel that these two mechanisms can make a new species. I come to this conclusion because additional information is required beyond what these mechanisms can provide. In the case of mutations we have some pretty good numbers on mutation rates and mathmatical models which we could use to see if the populations or time required match the limits of this world. In the case of transfer of data this mechanism does not create new information. Now you could argue that it does by flipping DNA and injection of partial chunks of DNA and related parts. The problem with this is the requirement to also have the appropiate start stop codes on the sequences and the appropiate turn on and turn off molecules that they must have to function. With this in mind I go back to other mathmatical models which show that the populations and time limits of the world will not allow this to happen.

The proof of evolution that I requested for the step by step sequence from one species to another is fair question for me to ask. Now I acknowledge that it may be so difficult that it may never be done. In my view it will never be done for other reasons but I realize just how big a problem it is to do this task. That being said I am ready to discuss evolution in other terms. If we limit our conversation to the above mechanisms we may be able to have a productive discussion.

[ARWallace]

Frank:

Thank you for your thoughful response. I am sorry that I assumed some things from your post. Evidently I put two and two together and came up with seven. I will try and be more careful in the future.

That's OK. It's just that I am usually pretty intentional and specific about what I say specifically so that little room is left for misinterpretation and misunderstanding.

I think we are getting somewhere in this dicussion. I would suggest that we keep the discussion somewhat at a higher level and not get too washed in detail. I think this discussion is being read by people with a wide range of backgrounds and if we keep the post at a description level it would help me and possibly others.

Well, apart from not knowing exactly what you mean by "higher level" - I would say that we get as detailed as we need to get. I mean that in no confrontational sense - only that I don't know who is reading our exchanges and at what level they are operating. And the stuff we're starting to wade into is best understood at the specific level. If anyone lurking wants to chime in for clarification, I am happy to respond in ways that are accessible to them. You are, by admission, well versed in molecular biology. When we are talking about the genetic bases of evolutionary change, it starts to become necessary to get into some pretty specific molecular biology pretty quickly. So let's proceed and see where we wind up.

I am familiar with the basic mechanics in molecular biology, it seems you are way more knowledgeable about a wide variety of species than I am.

Well, I profess no expertise in such matters. I find them interesting. I have wrestled with them at some length. And I have read a little and thought a lot. But I'll bet that's true of 99% of the people on this board.

To get from one species to another requires some massive (number of neucleotides) changes in DNA and support structure.

Well, to get from a common ancestor of all birds to the diversity of birds we see today, that is true. But in fact very little change to some very important regions of DNA can lead to profound changes in a very short amount of time. And this, in turn, may produce one or more new species.

Now I know that many mechanisms have been identified which may allow a transfer of information from one cell into another. This can be injected, it can come from flipped parts of DNA, and can just be duplicated.

Again, I assume you are using "information" and DNA interchangeably. I'd prefer to use just DNA since (a) it is more biologically correct and (b) it is not loaded with any baggage associated with the word "information" as it is used in the common vernaculum. But yes, DNA can become incorporated in a variety of ways and this may, in turn, alter genes, add genes or change the way they are expressed. And of course this can and will have effects on the organisms' phenotype, morphology, physiology or biochemistry. And we all know that changes are the stuff that natural selection acts on.

So from my perspective there are two evolutionary mechanisms that could produce new species, one being mutations and the other being a transfer of data.

Well, technically neither of these produces a new species. It is genetic change coupled with selection. This change can arise from point mutations (rather important when they happen in areas like genes that make proteins or regulatory genes), chromosomal changes (such as inversions or translocations), horizontal gene transfer from endogenous retroviruses and retrotransposons, gene duplications (with subsequent modification of the copy), and overprinting mutations (point mutations causing new start codons and new reading frames). And here's a pretty interesting example of an exchange of genetic information (not necessarily resulting in speciation - but certainly evidence that "information" can be added to genomes in a useful sense). Two researchers studying the alcohol dehydrogenase gene (Adh) found on chromosome 2 in fruit flies found that 2 species had a similar locus on chromosome 3. They sequenced it and found that it lacks the introns (regions that are cut out of mRNA before translation) found on the gene on chromosome 2. They proposed that it arose when the mRNA from the Adh gene was reverse transcribed (much like the HIV genes are) and inserted into a new region on chromosome 3 in these species. In other words, mRNA was made, introns cut out and this mRNA transcript was reverse transcribed to DNA and inserted in chromsome 3! Now - does this gene have a function, or is it merely extra DNA? Another study sequenced DNA in this region from a number of different individuals to look at the different forms that this new "pseudogene" took in a population (i.e. what different types of alleles were present). They found that the overwhelming majority of mutations were silent - just like the type of variation that usually exists in functional genes (i.e. they are tolerated because they have no deleterious effect on the protein produced). So there you have it - transfer of a gene from a most unusual source resulting in a new and functional gene in the host. Granted it is not speciation, but if this is not an increase in the sort of information some people feel never occurs, then I don't know what is.

In the case of transfer of data this mechanism does not create new information.

Respectfully, I disagree. See above.

The problem with this is the requirement to also have the appropiate start stop codes on the sequences and the appropiate turn on and turn off molecules that they must have to function.

Well, assume you are unconvinced by my fruit fly example. What about this study that suggests new genes can arise from overprinting?

The proof of evolution that I requested for the step by step sequence from one species to another is fair question for me to ask.

Well, fair and maybe not-so-fair. Here's my perspective - it's a fair question for anyone to ask. But it is unlikely that - even impossible - that science could ever provide an answer for reasons I described in my previous post.

That being said I am ready to discuss evolution in other terms.

Sure. What do you propose?

[frankbaginski]

ARWallace ,

When I said between one species and another I was refering to a wider gap than between two frogs or two birds. Just raise it up a level and I would be happy with that.

When it comes to sharing DNA with other species we will be looking at some pretty wild stuff. This of course did not happen with the first cell but I will take on the current interaction of species as our starting point since we know so much about these processes. This should be fun.

Too much time watching football this weekend. Go Packers.

[Kurieuo]

Kurieuo -

Thank you for a very thought provoking response. I sort of kicked things around yesterday after reading it. Here are a few responses I had: first, I agree that the identity of the designer is not one left to science. But it, and several related metaphysical questions will arise, and it is human nature to want to answer them. I applaud the open-mindedness with which you are willing to let the chips fall where they may vis-a-vis the identity if the designer. I am a little more concerned about the impact and potential deviseness such an identification might have. But fortunately I think that the answer to such a question is beyond human capacity to answer. Short of a microscopic image of a bacterial flagellum with "Made in China" stamped on it, I can't imagine what test could be applied to identifying the designer of such a structure.

Second, I am not certain that the studies you cited necessarily represent the relaxation of certain ideas that dominate science - that the authors of these studies reached these conclusions by invoking the notion of purposeful design. Finding a use for a structure that did not previously have a known use is - or at least may be - nothing more than the logical outcome of scientists studying a structure more closely.

I would agree with you. I do not believe a relaxation of certain ideas, which I understand as "acceptable philosophies", has happened in science, yet. Further, the studies mentioned, I agree, were simply a logical outcome of scientists studying a structure more closely.

What was the intention of quoting such studies then? I previously noted that "if only freedom of thought in science was always allowed these conclusions would have likely been reached much earlier." Perhaps there is an implication in that statement that freedom of though is now allowed, but it was unintentional. The word "always" should have in fact been left out, for I do agree more with what you say here. However, my point that there are benefits to conceding the intricate purposed design of something, even presuming the design, that such can have many benefits to a scientific investigation, still stands.

Regarding the appendix; research as early as 1980 confirmed that the appendix may have some as-yet unknown function as opposed to being a vestige. This study merely elucidates what that function is. As for junk DNA - well, because of a rather unfortunate case of poorly considered nomenclature, has been poorly understood by both scientists and laymen alike. I imagine the name arose from a rather narrowly focused group of biologists who study gene function or protein analysis. Because such DNA is not transcribed or translated, they could see no immediate function since DNA's only perceived role in their estimation is to carry instructions for making proteins. Geneticists who study chromosomes have long argued that this DNA may help space out genes increasing the chances of recombination. But the name junk DNA stuck. And the fact that all that allegedly useless DNA is there to begin with rather begs the question of whether a function(s) do/es exist. And it is this quest for knowledge that likely resulted in the study you cite as well as a host of others that describe possible functions for it. I don't purport to have any special knowledge of the motives of the authors of these studies, but I am not certain we can conclude that (a) the scientific community suppressed study of, nor was disinterested in the possible functions of these, or other structures; or (b) that a desire to see all of nature as the product of purposeful design motivated them. It may have, but scientists are a rather curious lot who continue to dig deeper rarely accepting the fact that the book is closed on anything in nature.

Whether or not the authors of the studies were trying to suppress functionality in these particular cases I think misses one main point I was alluding towards. My main goal was to show how ID could positively influence scientific investigation, and that it was not just a matter of identifying if biological systems exhibit intelligent design (of which IC is one suggested sign), but that once identified is actually spurs on investigation regarding what its purpose actually is.

Zoegirl hit another nail on the head with something I was alluding towards which is that certain assumptions of philosophies impact upon the way one examines the world around them and conducts their science:

It certainly shows that there have been assumptions made about the functions of organs based on their belief (theory, whatever) that these structures are simply mere remnants of evolutionary heritage without a purpose. To some degree, I think the discovery of a purpose of supposed junk DNA remained undiscovered and unexamined so long because this idea of "junk" DNA fit the preconceived notions of products of evolution. "Of course, evolution would produce junk DNA...." And this kind of bias can limit discovery just as much.

Now, the vestiges of hind leg bones in boas and the degenerative eyes of cave dwelling fish seem to be - in every sense of the word - vestigial structures. That they may have some, as yet unknown purpose that science does not understand does not detract from the fact that they are reducted structures that exist in operational form in closely related species.

Yes, these present more neutral scenarios, that is, assuming no design appears to have little if no impact upon the presumptions made about their functionality. I do not wish to debate however whether vestigial structures have in fact occurred due to evolutionary factors. It was neither my desire to focus on the negative aspects of only assuming naturalistic conclusions, but rather I desired to highlight to positive aspects of allowing true design to be identified and assumed.

My whole goal was to respond to your statement: "Merely identifying IC structures is a fairly mundane and ultimately uninteresting task." My summarised response to this particular point was: "When we see something that seems odd or useless, but such appears to be designed, then maybe we are missing something like was missed with Junk DNA, the human appendix and many other "vesicle" organs. ID inspires investigation once something is identified as expressing irreducible complexity or specified complexity, that is, when something has been identified as exhibiting signs of intelligent design."

And if the question of what junk DNA may do interests you, I recommend this review article from Scientific American.

It looks interesting and I will certainly give it a read over.

[ARWallace]

Frank:

When I said between one species and another I was refering to a wider gap than between two frogs or two birds. Just raise it up a level and I would be happy with that.

I am not sure that I follow. You said earlier "Now I don't feel that these two mechanisms can make a new species. I come to this conclusion because additional information is required beyond what these mechanisms can provide." and "The problem with this is the requirement to also have the appropiate start stop codes on the sequences and the appropiate turn on and turn off molecules that they must have to function." I provided you with an example of just this - "information" (viz. a functional gene) being added and expressed. Moreover, early on in this thread I provided some studies that showed that modification of two developmental genes provided morphological changes that resulted in a large number of speciation events in stickleback. So my questions to you are: (1) do you dispute the findings of the studies I have provided? And if so, in what ways? and (2) by "raising it up a level", are you suggesting that I provide the genetic bases of speciation from a frog into a bird (as opposed to between frogs or between birds)? I guess I am not sure what you're looking for here.

When it comes to sharing DNA with other species we will be looking at some pretty wild stuff. This of course did not happen with the first cell but I will take on the current interaction of species as our starting point since we know so much about these processes.

I agree that this is "wild stuff". But I am still a little unclear about what you mean by "interaction of species". Could you clarify or maybe give me an example?

And I'm still curious about your opinion on this question "given what the Supreme Court has ruled as opposed to what we'd like them to rule, do you think all models of creation should be taught (or none at all) to avoid violating the EC?"

Too much time watching football this weekend. Go Packers.

Well, I'm a Seahawks fan myself, but find it hard to get worked up about football. Besides, the superbowl is over. The Pats have taken football and Boston has taken baseball, and even the Celtics are playing respectable Parrish-Bird-McHale era basketball. Kind of takes the fun out of being a sports fan. Oh well. There's always NCAA.

[ARWallace]

Kurieuo:

Well, I think we agree more than we disagree, and I may just be arguing semantics. But let me clarify my position a little more clearly: I believe that science has a long track record of writing things off as disinteresting or uninformative, only to find later they were wrong. So in this limited sense I agree with you - haste make waste, and we ought not assume that because something does not, as yet, have some function or some purpose that we know of, that it does not. Zoegirl said it best when she said an argument from personal incredulity is a limiting one. But I think this is simply an artifact of the way science is conducted - after all, imagine if you were a biologist studying gene function. There's all this noncoding DNA cluttering up the genome. It doesn't produce proteins, so it isn't of direct interest to you, and why should you spend X years and Y dollars studying something you weren't awarded a grant to study in the first place? I can't fault a scientist for dismissing something they aren't directly studying. Science has limitless questions, but limited number of people to answer them, and very limited amounts of money to spend answering them. So it is for these reasons that I think science mistakenly avoids finding answers, and perhaps not because they feel everything should be purposeful or designed for a reason.

Moreover, scientists have even argued that something could evolve accidentally, and subsequently gain a function or purpose. Stephen Jay Gould argued this in his paper The Spandrels of San Marco and the Panglossian Paradigm. Gould felt that much like the spandrels in the central dome of St. Mark's Cathedral in Venice that have the appearance of purposeful design but are merely architectural artifacts of structures supporting the dome - that some biological structures may arise coincidentally with the evolution of other structures and assume another function. Gould termed these traits and structures exaptations. The idea is not without its controversy, but I would argue that scientists are, on occasion, capable of thinking outside the box.

Now, as for the question of IC and ID structures; I am not certain what information we could glean from them once they were identified. But maybe this is a limitation of my own imagination not being an expert in the field, and part of it may be my belief that the identity of the designer is germane in answering some rather important questions. As for how these structures arose - I think we have a conundrum. Either the designer fashioned them together, de novo, from completely novel structures that did not exist hitherto in nature (in which case we'll never know how it all happened), or the designer tweaked and modified existing "stuff" to make the IC structure...which would be indistinguishable from naturalistic processes. And if we have naturalistic explanations, then the law of parsimony suggests that we don't need to invoke a designer (at least this is an argument I can imagine a dyed in the wool methodological naturalist studying such structures would invoke). And as for the why question - either we need to know the motives of the designer (which may be difficult or impossible to ever know), or we assume they arose because the designer seemed to think this would confer some benefit on the owner...which again is a naturalistic explanation (of the "natural selection favored it" variety). I say none of this to be argumentative. I'm just not sure what mechanistic or biological information can be gleaned once an IC structure is identified. And certainly the metaphysical questions are equally as provocative.

Well, I painted myself into a corner here. Thank you for your patience as I work some of this out!

[zoegirl]

Hey, I remember reading the Spandrels!! Had to read it for my "Mechanisms in evolutionary physiology" class in grad school.

It was a fascinating read, I'm not being facetious here, I did find it well-written and interesting.

[ARWallace]

It was a fascinating read, I'm not being facetious here, I did find it well-written and interesting.

It's impossible to read Gould without a dictionary and a thesaurus. And even then I struggle.

And he was just as articulate in person. One smart guy - and a big loss to science.

Did you happen to read any of the articles he wrote each month for Natural History?

[zoegirl]

Oy, my reading then was dictated by my classes (research journal articles....ad nauseum ) and the occasional review article.

Good reading, mind you, just tiring....that was on eof my better classes....learned a Lot in that class.

And I must confess I haven't kept up since then (finished last summer....yay)....teaching schedule I am hard pressed for all the books I have on hold, let alone keep up with research, although I try.

And those magazines, especially the journals, are expensive!!

[frankbaginski]

ARWalace,

You said:
"I agree that this is "wild stuff". But I am still a little unclear about what you mean by "interaction of species". Could you clarify or maybe give me an example?"

I was refering to the point in our past when there was but one cell (assumed Darwinian past). At that point there were no other species in which to borrow DNA from. The point I was making is that at the start the mechanics were limited. But since we have no data on the first cell I am more than willing to start with our current mix of species.

[Himantolophus]

Darwin's theory starts with a cell and all species come from it. Are you saying all information was in the first cell? That means all protein sequences, genes, etc. If so you agree with JAD. If you think that information is not required then you have not thought this out. And don't give me that natural selection makes information nonsense.

I apologize... I was talking about the evolution of new species and not new families and phyla. It is obvious that single cells have vastly simplified genomes from higher organisms so there must have been some addition to the genome as you went from cell to multicellular to invert to vertebrate. There is no evidence for an ancient "super-cell". I still hold that gradual additions over long periods of time could provide the required material. The Darwinian mechanism may not be the best explanation (as for random chance) but I'm sure the answer is still out there to be found. Maybe there is another mechanism for "kind to kind" change that has yet to be discovered. Whether God is involved or not is unknown. Simply not knowing the answer doesn't devalue macroevolution, it just means we don't know it yet!

My reply stands for species --> species evolution however...

I think we should agree to disagree.

I think we've come to that conclusion already

I hope you were refering to errors in science that science can correct. It reads like you were saying science can fix the Bible. I will assume that you were refering to science.

yes, i meant science can correct it's errors. No one can change the Bible's words... I meant that it is up to the reader to ponder their interpretation of those words.

Since he wrote his theory we have found millions of fossils and the picture has not changed as he predicted. One of the ways to check a theory is to see if it has the power to predict things. Darwin's theory predicted just the opposite of what we found. Now some people think that the discovery of DNA supports Darwin's theory. Myself and some others feel just the opposite. The complexity is so vast that simple steps can't make the end products we see around us today.

What exactly is "opposite" to what Darwin theorized? Because he mechanism is almost impossible to test in the lab (long time tables) so that is up in the air. His observation of change over time are matched by the fossil record. Genomics has embraced evolutionary theory without any problems. I also don't see tiny changes adding up over time to equal bigger changes as that implausible. DNA started out very simple and compiled it's complexity over long periods of time. Looking at it as a human in the 21st century at the pinnacle of the evolutionary ladder, of course it's complex! Maybe if all species had vastly different genetic makeups, but we're all working with the same molecules! I know you have a different view on both the fossil record and DNA so I'll stop here. I'm sure you have knowledge on this subject.

To everyone here:

The main thing I want to know is... where do you draw the line in microevolution? Where does it cease to be "micro" and be "macro"? If you think selection and mutation are insufficient to create new species, then what mechanism creates them? We know they don't just appear out of nowhere. What about all the transitional species in the fossil record? If they were created, then why with such awkward designs? ID's and creationists admire the "design" of nature, but what if it was created by evolution? And if God created evolution, then we are still admiring that same design. With all the "problems" you say evolution has, what about the "proof" and "testability" of creation and ID? Comparing the two, it seems like evolution is the winner simply by default!

[ARWallace]

Frank:

I was refering to the point in our past when there was but one cell (assumed Darwinian past). At that point there were no other species in which to borrow DNA from.

Well, I am unaware of any model that proposed that there was only one, ancestral cell. Most models propose that organic molecules were produced by inorganic precursors. These building blocks assembled themselves into short polymers - some of which (e.g. RNA) were capable of self-replication and even producing proteins that may assist in their replication. These entered small lipid spheres where they were protected from their environment - and at this point there was small proto-cells with variable replicating genetic material. Moreover, even prokaryotic cells are capable of exchanging genetic material through transduction, transformation and conjugation. In fact, these methods account for rapid changes in bacteria by generating new genetic diversity. In the case of antibiotic resistance, plasmids containing genes for resistance are routinely exchanged with bacteria lacking the resistance. So unless I am missing something, we do have ways of creating new genetic diversity, even at the earliest times in organic evolution (assuming a "Darwinian past").

But I, too, am willing to work with our current mix of species if this helps.

[ARWallace]

Himantolophus:

Looking at it as a human in the 21st century at the pinnacle of the evolutionary ladder, of course it's complex!

What makes you think humans are the pinnacle of the evolutionary ladder? Isn't evolution more routinely described as a bush, and not a ladder upon which one ascends? This sounds a little like Aristotle and his scala naturae.

And for what reason(s) do you place humans at the top?

Just curious.

[Himantolophus]

What makes you think humans are the pinnacle of the evolutionary ladder? Isn't evolution more routinely described as a bush, and not a ladder upon which one ascends? This sounds a little like Aristotle and his scala naturae.

And for what reason(s) do you place humans at the top?

maybe I should have put "evolutionary rhododendron" haha

sorry I didn't mean to word it quite that way but humans are easily the most sophisticated and intelligent creatures on the planet. The fact that we have placed ourselves above natural selection alone puts us above all other creatures (evolutionarily speaking). Yes, all the other evolutionary lines (mammals, reptiles, birds, amphibs, fish, inverts, bacteria, etc.) have evolved alongside us, but none has come close to us in our ability to dominate the planet (well maybe bacteria, rats and roaches)

[ARWallace]

sorry I didn't mean to word it quite that way but humans are easily the most sophisticated and intelligent creatures on the planet.

Indeed. But "pinnacle of evolution" is a rather loaded phrase, I think. It may seem a little presumptuous to assume that we are the best that 3.8 billion years of evolution has to offer. I think it is fair to say that we are just as evolved as bacteria (they have, in fact, been evolving far longer than we have). But it is also fair to say we are more complex (however this metric is measured) than many other organisms. And I think it is further fair to say that if we turned the clock back a few billion years and let it all happen again that there is no reason to expect two big brained primates ought to be the ones having this discussion.

The fact that we have placed ourselves above natural selection alone puts us above all other creatures

I think that this, too, may be another another claim that needs qualification. On what basis do you think we are above natural selection? In what way is evolution not working itself out in the AIDS epidemic? How about the thousands of people who die each year in the US from influenza? Or the millions who die of starvation and diseases such as dysentery, malaria, yellow fever, Dengue fever, pneumonia, tuberculosis and various and sundry viruses causing encephalitis? And what of those who contract but do not succumb to these diseases? And do you think it is a coincidence that the distribution map showing the areas where malaria is endemic mirrors the distribution map of sickle cell disease quite closely - a disease that, in its heterozygous form affords some resistance to the malaria parasite? Paul Ewald has argued fairly convincingly that not only are humans subject to evolution, but that current human practices and behaviors affect both our predisposition to contracting contagious diseases as well as the degree of their pathogenicity.

Now, I think it is fair to say that we are unique among other species in our ability to manipulate our environment in ways that often benefit us - and further, that we are able to treat disease and allow alleles that might not otherwise get passed on in wild populations to get passed on. But I think we are far from "above" natural selection, and possibly it may be that we are manipulating our environment (albeit inadvertently in most cases) in ways that bear rather directly on human evolution. But that's just my opinion.

And yes - I think roaches, rats, bacteria and possibly a few insects and maybe even house sparrows are pretty dang good at survival.