Darwin is Dead – Part One – Montana T-Rex edition

This Carnival is a bit different, being presented in more than one post. The star of this portion is Matt aka IAMB, who is the host of the Pooflinger’s blog. So with no further ado, Matt:


Cretaceous Squishies

Not long ago, an article in Discover Magazine devoted to the work of Dr. Mary Schweitzer turned up (she was the one who found preserved soft tissues in a T. rex femur, for those who don’t remember). This prompted me to predict a resurgence of creationist interest in Schweitzer’s work, given the original reactions from the folks at places such as AiG (heads-up on the link: fairly vulgar language).

I wasn’t entirely accurate with my crystal-ball-gazing, as none of the big creationist organizations had anything to say this time (that I’m aware of), but I wasn’t completely wrong either. Eventually, the find was mentioned by a forum poster, and then soon after by a commenter on this very blog, which led to a bit of discussion. Said discussion included several references to claims made about the find by creationist sources, as well as the obligatory references to TalkOrigins’ response. As most of us here should by now be familiar with our host’s reluctance to visit the T.O. archives for any reason (which is fair, since some here would probably sooner experience an appendectomy sans-anesthesia than willingly visit AiG or ICR), I decided that another route would be necessary. That in mind, I offered to forward Dr. Schweitzer’s actual peer-reviewed research papers to our host if he wanted them. Unsurprisingly, he responded via email almost immediately. This led to an ongoing conversation, the climax of which was the decision that we should both read the same material and post our thoughts on the same day and in the same place (that place being here and that day being today). It is a given that both Radar and I will come to different conclusions about the same stuff, but I am curious to see just how different we see things. So, without further ado, I present my thoughts from the mainstream science side of the equation…

The first thing many a creationist will ask is how, if the earth is as old as science says, could soft tissues be preserved at all? The remarkable preservation in this case can partly be explained by several factors: the bones of MOR 1125 (the actual designation of this particular specimen… easier than saying “the well-preserved T. rex”, though I could call her “Tyrannosaurus Fresh” or something…) were quite heavily mineralized… that is to say: very densely fossilized… which helps to protect the internal tissues from outside elements. Another factor is the very dense nature of theropod bone in general, and that the tissues were found inside the femur of the specimen. Since that particular bone just happens to be quite massive in the first place, internal tissues are quite well protected. Beyond those couple factors, there most certainly things about the fossilization process that we don’t know, but it gives those in the paleontology field something new and fascinating to work on. Job security!

One point I should probably state in completely unambiguous terms is that these “preserved soft tissues” were by no means “fresh”, as some creationist sources have indicated in the past. The fragments of endosteal bone tissue containing the soft tissues were demineralized over a period of seven days to separate bone from soft tissue. Once rehydrated, the soft tissue vessels were shown to be fairly resilient, as well as elastic, and could be stretched much like a rubber band. Found within these vessels were a number of structures that appear to be preserved blood cells, some containing interior structures that appear to be possible nuclei. However, it would be unwise to get any Jurassic-Park-style hopes up, as finding anything more than very fragmented DNA chunks is improbable in an extreme sense of the term.

The team has also identified protein fragments from bone samples. Some of these samples produced a slight immune system response when injected into rats… a response generally triggered by foreign hemoglobin. One creationist with whom I’ve previously discussed this portion of the testing indicated that it would be impossible for hemoglobin to survive the long ages accepted in science, so a young earth was proven by this test alone. Unfortunately, this is not the case. The test in question would also produce the immunological response without actual hemoglobin, needing only a fragmentary part (known as a heme) with a couple of amino acids still attached. Unlike actual hemoglobin, a heme is quite stable and is basically an iron atom surrounded by four nitrogen atoms surrounded by an organic ring (mostly various carbon-hydrogen molecules of varying mass) and is the part of the hemoglobin that actually binds oxygen to red blood cells. We also know of several amino acids that have very good long-term survival abilities, so it is possible for these things to be found in a 60myo specimen, though definitely not common.

The response from the creationist to this information was to ask why the lab would test for hemoglobin via immunological response if they knew that a few stable molecules would give a false positive… and that the whole thing seemed like a cooked-up explanation for something that evolutionary timelines couldn’t account for. This is incorrect as well, as you will see. The reason to run such a test, knowing full well that something other than hemoglobin can cause a positive, is to determine if what you have is actually still organic… or just a fossilized representation. Don’t laugh: fossilized muscle, hair, feathers and even blood cells have been found before, but in most cases are entirely mineralized with no organic traces remaining. The immunological response demonstrated that the sample was indeed still organic in nature (as if the elasticity of the tissues wasn’t enough, but with one’s professional reputation at stake, one can never be too careful).

Another fascinating thing about this find I hinted at earlier, when I called the specimen “she”. This specimen possessed a different sort of bone tissue on the interior of the femur than other described bone types… a type found in avian medullary bone. This particular bone tissue forms naturally in the long bones of female birds during ovulation as a response to increasing levels of gonadal hormones, and provides an easy source of calcium that birds need for the formation of eggshells. What does this say to us? Not only was our 1125 a “she”… she was knocked-up as well (hard time finding contraceptives in those days)!

Both the previously-mentioned soft tissues and the medullary bone samples were compared against femoral tissues from modern birds, and striking similarities were found between the samples and similar tissues from the modern ostrich and emu (which was predicted, since the ostrich and emu share many structural traits with theropods… part of the reason scientists began to suspect the dinosaur-bird link in the first place). In fact, the evidence for the dinosaur-bird link had grown so much prior to this find, that scientists had predicted the presence of avian-type medullary bone in theropods. This find vindicated that prediction, and further solidified the dinosaur-bird evolutionary link, as well as demonstrating that an emu and a T. rex have more in common (from an evolutionary relationship standpoint) than a T. rex and an alligator.

To some, this may be a surprise. To others, not so much. Next time you’re around an emu (at a petting zoo or similar place), take a good look at them: their eyes, how they walk, etc. There’s something primitive about those birds that speaks to me of a time long-gone… a time when the earliest hamster-sized mammals spent their days hiding from the dinosaurs who would find them to be a tasty snack, and dreaming of the days when they might be able to come into the light and take over. Perhaps some bit of those primitive mammals still remains within us, for that is the part which speaks to me whenever I see an emu stalking along the fence at the local petting zoo, studying the running children in a way that makes my blood run cold. That particular bird in my mind looks at kids in a way that (to me) says “if only I had teeth…”

Anyway, I guess now would be a good time to stop polluting Radar’s blog with my evilutionist tripe and head back to my own little corner of the web. I’d like to thank our host for this opportunity to hang out here for a day, sharing ideas and promoting discussion. Hopefully this won’t be the last time that he and I can do something like this, but I think I’ll let him pick the topic next time… and don’t worry: I’m not going soft on you or anything… I’ll still be flingin’ the poo on a regular basis as always. Anyone with questions is welcome to ask in the comments here or email me (you can get the addy from the sidebar on my blog).

Written by IAMB… posted by Radar.

Thanks to Matt. Be sure to check out his blog! Now, independently, I also created a post concerning the same subject. Matt did not view my post, nor did I view his. Here is my take on the same subject:


The Montana T-Rex, Colonel Sanders, and a dilemma

I first became familiar with Avian Medullary Bone (MB) in fourth grade. As it happens, the test-makers in my school district had identified a set of children who were supposed to be 1) advanced or, 2) trouble-in-the-making. Whatever the criteria, I was selected and my parents agreed that I would go to a new school with an “enriched” program. This meant I had to leave behind my buddies, which wasn’t pleasing to me. But I was fortunate in that the school was not much farther than my neighborhood school, still within walking distance, and I soon made a new group of friends.

The enriched program was primarily intended to introduce us to high-school level math and science courses while still in grade school, so that we would take advanced courses in high school and be ahead of the game for college. Therefore, I was taking a biology course while in fourth grade. Here is where Colonel Sanders comes in.

We were taught that one effect of nuclear attack would be that radiation would kill off our body’s ability to make new red blood cells, thus causing death. Of course there were many other effects of nuclear war that were discussed as well. But this one got me to thinking….I learned that red blood cells were produced within the bone and therefore I decided that if I ingested the “engines” that produced red blood cells I would have a better chance for survival. This is how I began a habit of breaking open the “drumstick” (femur) bones of my fried chicken and eating the marrow contained therein. Later I realized that this was a useless endeavor but having acquired a taste for the marrow, kept eating it for several years, until the marrow began to look less appetizing to me and I discontinued the practice.

In any event, fourth-graders can take raw information and go wild with it, if they have a vivid imagination. Whereas I soon realized the stupidity of eating dead, fried chicken bone marrow in order to withstand a nuclear blast, it was all part of seeing how immensely complex living organisms are. I also had become very familiar with the interior construction of chicken bones, cooked.

It was therefore no random thought that came back to me as I viewed pictures and read text concerning the T-Rex bone being studied by Mary Schweitzer and colleagues at Montana State and North Carolina State Universities. My early mistake concerning bone marrow was simply a bump on the road to learning more about how life works. I took every biology, chemistry and physics course I could get my hands on in both Junior and Senior High and also continued my studies at the University until I was abruptly drafted into the military. My career focus took a drastic turn at that point and science became a hobby rather than a vocation.

Mary Schweitzer is apparently a dedicated scientist who is not particularly fond of public scrutiny, not the “Star Search” kind of scientist you often find. To me, this makes her work even more interesting. I was pleased when Matt Ford sent me a couple of documents detailing work that she had done with Museum of the Rockies (MOR) specimen 1125, a Tyrannosaurus Rex estimated to be 18 years old, plus/minus 2 years.

Now, there were those in various camps, the creationists among them, who began to hail the result of the studies done by Schweitzer and her team as the discovery of dinosaur DNA. I will be publishing the text sent my by Matt so that the reader can view the same documents that I have read. Whereas it does appear that MOR 1125 may have blood cells preserved, at least in part, along with other cellular materials, this has not been the initial focus of Schweitzer and her team. They have been comparing the remains with the femur bones of living female birds and finding similarities that indicate that MOR 1125 had an eggshell-producing factory that is very similar to those of some modern birds, such as the Ostrich. The team is apparently excited about this, since no other living creatures other than living and egg-producing female birds have this kind of MB structure.

Mary Schweitzer is a strong advocate of the dinosaur-to-bird evolution model and gives her findings within that context. For evolutionists, this is good news and is in keeping with the evolutionary models they propose. For creationists, this is another example of God’s use of similar systems in differing kinds of creatures. Like much of what science continues to discover about organisms both ancient and modern, your expectation and belief color what you believe to be the result.

It seems that blood cells and possibly DNA may also be preserved in MOR 1125. Many creationists have asserted this, myself included, and stated that current studies indicate that DNA cannot be preserved past 10,000 years, unless preserved under very special circumstances not found in Montana, and even then the barrier only moves up to 100,000 years. Yet as of this time it is not certain that DNA has been preserved nor has any been isolated within this specimen. It was not the initial focus of the team to pursue this and as of this writing no certain statements have been issued. It is my understanding that preliminary findings indicate that DNA may indeed be found. If so, then this will be a problem for evolutionary thought unless they can show that DNA can be preserved for millions, rather than thousands of years.

Here is the dilemma. I ask this of myself and not just the reader. What would you do if you were presented with evidence that completely blew away everything you believed about a subject, one that was vital to your very philosophy of life? This has been the subject of novels and one that I may write on someday. I applied it to this situation. What if Mary Schweitzer and colleagues were to find compelling evidence that this T-Rex fossil lived less than 10,000 years ago? What would this mean to her and to evolutionary thought? Could she, and they, publish such findings and begin to adjust their thinking accordingly. Or would they quickly bury the evidence and agree among themselves never to mention it again?

One of my commenters asked me what I would do if I discovered that life had, indeed, evolved over millions of years. Would I lose faith in God? No. I would have to re-address my understanding of the Bible, certainly, most especially the Old Testament books of Genesis and Job. I would have to admit that I misunderstood the Bible, thought that symbolic and allegorical language was historical, and go on from there. It would certainly be tough to adjust but doable. But the better question is, what if I found the evidence myself? Would I publish it? Or would I hide it?

One never knows what you are in an emergency until you are actually tested. Those of you who have faced combat or a chaotic emergency in civilian life know what I mean. You are either a quick decision-making and acting machine, or one of those who tends to be rooted to the spot in fear or confusion. Perhaps finding evidence that shakes your foundational beliefs is similar. Maybe you really don’t know until you are in the situation.

If Mary and her team find compelling evidence that tends to disprove evolutionary thought, I can simply hope that she/they will be willing to share the evidence with the world and let the chips fall where they may. Thus far, they have published interesting results that hint at other things but also tend to agree with standard evolutionary thinking. I will be awaiting with interest the findings concerning the possibility of DNA being preserved. Either way, I’ve sworn off eating chicken bone marrow!

By radar and also submitted to Matt’s blog for posting should he choose to do so.

One of the papers referenced by Matt and myself can be found here.

An associated article is here.

PZ Myers posted this about that.

Now, a companion piece for the subject at hand from Daniel Criswell:

How Soon Will Jurassic Park Open?

In the fictional movie “Jurassic Park” dinosaurs were cloned by obtaining the genetic information necessary to make a dinosaur from ancient DNA (aDNA) sequences extracted from dinosaur blood found in the gut of mosquitoes embedded in amber. Although most scientists still consider the science in Jurassic Park fantasy, acquiring dinosaur DNA has become a possibility over the past few years based on the attempts of sequencing small pieces of aDNA from archaic man and animals. Is it possible that aDNA and other biomole-cules such as proteins in extinct organisms could survive environmental conditions well enough for thousands of years, or according to secular scientists, millions of years?

In March 2005, Mary Schweitzer and her colleagues published a paper in Science describing the presence of soft tissue (cellular material) in the fossilized femur of a Tyrannosaurus rex unearthed in eastern Montana.1 Schweitzer et al. reported the presence of structures that appeared to be blood vessels and blood cells with nuclei where DNA could be found. Many of the tissues could be stretched repeatedly and returned to their original shape indicating the presence of elastic proteins commonly found in blood vessels. Pictures of the tissue and experiments comparing the T. rex tissue with ostrich bone tissue appeared to confirm that the material was soft tissue. The presence of soft tissue, which decomposes rapidly after an organism dies, fits the Creation model (asserting that dinosaurs lived recently, in the last 10,000 years) better than an evolutionary scenario making dinosaurs older than 65 million years. However, the environmental factors responsible for preserving soft tissues in fossilized bone are unknown, and until they are determined, creationists as well as evolutionists can’t be sure if there is a mechanism that preserves soft tissue indefinitely. After all, until the Schweitzer discovery, it was not believed that intact blood vessels and blood cells, which normally decompose rapidly upon death, could still be in a dinosaur bone after even a few years—much less 10,000 years or 65 million years.

Is it possible this tissue still has DNA and proteins? Although it is unknown how soft tissues can be preserved in fossilized bone and how long they persist, DNA and protein degradation kinetic studies have been done to extrapolate how long DNA and proteins are able to last once an organism dies. These studies show that small DNA fragments (<500 base pairs) still retaining enough of their original sequence integrity to identify the organism of origin would have to be less than 10,000 years old if the specimen was preserved in temperate climates.2,3,4 The moisture or humidity surrounding the animal’s cells, and how fast the sample was fossilized would also influence the rate of aDNA decay. The environmental conditions significantly affect how long aDNA would be preserved and it is possible to extend the “life” of aDNA by lowering the environmental temperature.2,3,4 Molecular biology laboratories keep DNA indefinitely in a freezer at -80ºC (although no one, obviously, has done this for thousands of years!), and kinetic studies predict that at polar temperatures (-50ºC) the “life” of identifiable DNA may be extended to 100,000 years.2,3,4 The recent sequencing of 28 million bases of mammoth DNA extracted from frozen tissue likely confirms the assumption that DNA lasts longer at colder temperatures.5 Some proteins may last even longer (up to a million years) as small peptide fragments of the original complete protein. Other proteins such as collagen, a protein found in bone, probably completely degrade in less than 30,000 years, but this obviously is far less than the 65 million years given for the age of the dinosaurs.6

Once an organism dies, DNA immediately begins to degrade. The damage that DNA undergoes after the cell dies leads to many changes that can make determining the original sequence difficult. DNA is contained in chromosomes typically millions of bases long, but at death the chemical bonds that form the spiral DNA ladder rapidly breakdown leading to fragmentation of DNA into short segments less than 500 bases long.4,7 Two of the four DNA bases that compose the genetic code, the purines adenine and guanine, are lost over time from the original DNA sequence. Base modification of cytosine can result in base substitutions in the proposed DNA sequences that weren’t in the original sequence.4,7 These are just a few of the more common problems scientists face when trying to determine the original aDNA sequence from samples taken from organisms that have long been dead.

In spite of these problems, many short aDNA sequences have been published from a wide variety of fossilized and ancient organisms. Plants,8 bacteria,9 mammals,10 Neanderthals,11 and other archaic humans12 have had short aDNA sequences identified. Most of this aDNA information has been made possible from the multiple copies of mitochondrial DNA (mtDNA) that are found in each cell and the technology of the polymerase chain reaction (PCR). PCR is capable of amplifying millions of copies of a short stretch of DNA from just a few original aDNA molecules. The complete process of amplifying aDNA from an archaic source has many challenges however, and it is possible that none of the published sequences are valid. The PCR reaction is sensitive enough to amplify DNA from just one molecule of sample aDNA. This means that DNA contamination from humans and microbes that may already be present in the laboratory (from people simply breathing, microbes in the dust, or previous PCR reactions) may lead to amplification of the contaminating organism and not the intended aDNA.

Scientists working in this field have tried to establish a set of criteria that would insure the likelihood of valid published sequences.4 One of the conditions proposed is that any aDNA sequence needs to be reproduced in an independent laboratory. This is a basic premise of the scientific method stipulating that true scientific discovery needs to be reproducible, and this requirement is commendable.

There are many other guidelines for determining the validity of an aDNA sample; unfortunately, one of the guidelines used is whether the aDNA sequence in question follows evolutionary theory for the origin and time of the appearance of the organism being sequenced. This was evident in two cases involving aDNA sequences published for a putative dinosaur bone and a bacterium. In 1994, Woodward et al.13 reported that an 84 base pair sequence of the cytochrome b gene from mtDNA extracted from a bone sample found in Cretaceous rock was most closely related to mammalian cytochrome b DNA. Because of the size of the bone and its location in Cretaceous rock, it was assumed to be that of a dinosaur. Woodward was thoroughly criticized for his findings14,15 because (1) His work was not reproducible in an independent laboratory,
(2) dinosaur DNA could not have lasted that long (remember, DNA is degraded in just 10,000 years), and (3) “every paleontologist knows” that dinosaurs are more closely related to birds than mammals. One of Woodward’s most vocal critics was Mary Schweitzer working at the time for the Museum of the Rockies in Bozeman, Montana. Schweitzer and Blair Hedges wrote a rebuttal to Woodward’s work declaring,

. . . a putative dinosaur sequence would be expected to cluster with birds and crocodilians in a phylogenetic analysis of amniotes.14

In spite of the meticulous care that Woodward’s group had taken to insure there was no contamination of their samples, Schweitzer and Hedges (and others) contended that the mtDNA cytochrome b sequence was contaminated with human DNA because it was not independently verified in another lab and because their phylogenetic analysis grouped the putative dinosaur mtDNA cytochrome b sequence with human DNA.

In a similar case, Vreeland et al. published the complete sequence of the 16S rDNA gene from a Bacillus species of bacteria extracted from a putative 250 million year old salt crystal.9 Not only did they acquire an aDNA sequence that closely resembled modern Bacillus, but succeeded in culturing the organism. Again critics claimed that the cultures and aDNA samples had to be contaminated based on the assumption that a 250 million-year-old organism could not be that closely related to modern bacteria and culturing something dormant for 250 million years simply is science fiction. Vreeland’s claims have not been reproduced in an independent laboratory and many scientists in the field continue to doubt that aDNA can be extracted from organisms “millions of years old.”

In contrast to Woodward and Vreeland, sequences from Neanderthal mtDNA were used to calculate the DNA contribution that Neanderthals may have made to early modern humans in Europe.16 This study also has not been independently verified, but has been hailed as an example of how aDNA can increase the knowledge of early human population genetics because the data generated supports the evolutionary notion that Neanderthals were not ancestors of modern humans.4 The acceptance of unverified work because it fits evolutionary thinking and the rejection of unverified work because it does not fit the evolutionary paradigm is a disturbing trend that surely will affect future research efforts with aDNA samples.

The Schweitzer team is in possession of tissue that may provide more information about aDNA and the age of the dinosaurs. This issue is already settled in many secular scientists minds, but if Schweitzer’s team successfully extracts aDNA from the T. rex tissue it will either confirm that T. rex lived less than 10,000 years ago or send scientists back to the laboratory to figure out how DNA can survive 65 million years of environmental and geologic upheaval. If the aDNA extracted does not meet evolutionary presuppositions will the sequences be considered contaminated and go unpublished? Schweitzer acknowledged in a recent MSNBC interview that preliminary data collected were “intriguing,”17 as many scientist anxiously await the results of their biochemical analysis of the possible protein and DNA content from the
T. rex tissue and the implications of these results.

Although Jurassic Park will remain a fantasy about an amusement park full of living dinosaurs, watching scientists scramble to conjure up new theories explaining the new data provided from soft dinosaur tissue may be more interesting and more entertaining.

Read the entire article with all references here.

Dr. Carl Weiland makes the following notes:

“The evidence that hemoglobin has indeed survived in this dinosaur bone (which casts immense doubt upon the ‘millions of years’ idea) is, to date, as follows:

*The tissue was coloured reddish brown, the colour of hemoglobin, as was liquid extracted from the dinosaur tissue.

*Hemoglobin contains heme units. Chemical signatures unique to heme were found in the specimens when certain wavelengths of laser light were applied.

*Because it contains iron, heme reacts to magnetic fields differently from other proteins—extracts from this specimen reacted in the same way as modem heme compounds.

*To ensure that the samples had not been contaminated with certain bacteria which have heme (but never the protein hemoglobin), extracts of the dinosaur fossil were injected over several weeks into rats. If there was even a minute amount of hemoglobin present in the T. Rex sample, the rats’ immune system should build up detectable antibodies against this compound. This is exactly what happened in carefully controlled experiments.

Evidence of hemoglobin, and the still-recognizable shapes of red blood cells, in unfossilized dinosaur bone is powerful testimony against the whole idea of dinosaurs living millions of years ago. It speaks volumes for the Bible’s account of a recent creation.”

The entire post is here.

(original link)

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s