subscribe to the RSS Feed

Friday, August 29, 2014

Some Evolutionists Just Never Learn

Posted by jlwile on March 23, 2010

You would think by now that even evolutionists would finally admit that there is very little (if any) DNA in a living organism that could be described as “junk DNA.” However, they are still out there doing it. For example, in a rather pathetic attempt to refute Dr. Stephen C. Meyer’s book, Signature in the Cell, evolutionary biologist Dr. Francisco Ayala made the following statement:

There are also lots and lots of DNA sequences that are nonsensical. For example, there are about one million virtually identical Alu sequences that are each three-hundred letters (nucleotides) long and are spread throughout the human genome. Think about it: there are in the human genome about twenty-five thousand genes, but one million interspersed Alu sequences; forty times more Alu sequences than genes. It is as if the editor of Signature of the Cell would have inserted between every two pages of Meyer’s book, forty additional pages, each containing the same three hundred letters. Likely, Meyer would not think of his editor as being “intelligent.” Would a function ever be found for these one million nearly identical Alu sequences? It seems most unlikely.

But the fact is that functions have been found for these Alu sequences and other sequences like them. It is amazing that an evolutionary biologist doesn’t seem to know this.

These Alu sequences are part of a wider grouping of genetic elements called “Short Interspersed Nuclear Elements (SINEs).” They have been demonstrated to have many, many functions in the genomes of many, many organisms. In fact, Meyer catalogs five lower-level genomic formatting functions, four species-specific higher-level genomic formatting functions, and five species-specific RNA coding functions. Thus, it is Ayala’s claim, not the Alu sequences, that is nonsensical.

My point is not so much that Ayala is demonstrably incorrect. It is broader than that. There are large parts of the genome of every organism for which we cannot directly specify a function. However, the fact that we don’t understand the function doesn’t mean there is no function. Evolutionists used to confidently tell us that the human appendix has no function simply because they couldn’t determine one. However, we now know that the human appendix certainly does have a function, as creationists always claimed. Thus, the fact that we don’t know the function doesn’t mean there isn’t one.

So…is there some other way to determine whether or not parts of an organism’s genome are functional? I think so. The reason the cell can use the information encoded in DNA is that a process called transcription makes a copy (actually, a negative image) of the information, and that negative image is then carried out of the cell’s nucleus. Well, it is hard to imagine that a cell would waste all the energy required to make the negative image of a section of DNA and carry it out of the nucleus if that section of DNA isn’t useful.

This is the genius behind project ENCODE. The researchers in this project are finding out which parts of the human genome are transcribed. Assuming that the cell would not waste the energy to transcribe useless bits of information, the argument is that whatever is transcribed actually has some use and is definitely not “junk.”

Well, what has ENCODE found? In 2007, the group published its first major results. Here’s what the researchers say:

The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact.

In other words, most of the human genome is functional. This is yet another failed prediction of evolution. Evolution first predicted that organisms should be littered with useless organs. Indeed, Darwin likened such useless organs to the silent letters in a word – they tell you things about the word’s origin but serve no function. When that prediction was falsified, evolution predicted that the human genome would be littered with junk DNA. Project ENCODE seems to have falsified that prediction. Indeed, the data are telling us that the concept of “junk DNA” should, itself, be junked.

Comments

14 Responses to “Some Evolutionists Just Never Learn”
  1. Jacob says:

    Comments in older threads seem to be disabled. I hope that you don’t mind me dropping it in this thread. If you really want, you could set up a separate thread or do this through email. Move it, do whatever you want, but I do want to continue this debate.

    First, I know what you want, but you’re not addressing my point: what does this have to do with the theory of evolution? What I am saying is that, yes, I get that you want them to apologize, but your words speak of an indictment against everybody, which is inherently a contradiction. In the original post, you said that “it was considered so important” that it was made into a documentary, which implies that most scientists found it important instead of a couple of people who sought to blow it out of proportion. You do this again when you act like it was deemed “one of the most important fossil finds in history” via scientific consensus instead of hype by a select few. Then in the final paragraph you extrapolate all of this to mean that somehow evolutionists do not act scientifically, which is a pronouncement based on what you yourself call a small team. That is what I am objecting to. In fact, it is because of further scientific tests by people who had no stakes in the fossils that its true nature was discovered.

    Second, you totally ignored the Gallup poll. Do you care to refute it or not? Now, if 95% of all scientists in general agree with the theory of evolution, then we should expect that number to rise amongst biologists. By the Discovery Institute’s own count, they have about 700 creationists, which aligns closely with the numbers found in the Newsweek story. Even if you cast aspersions on this fact, then we still have the 95% figure. What kind of number do you yourself have to refute these claims?

    Third, I get the point of the Luskin article, but you didn’t get the point of my rebuttal. Evolution is a family tree, more or less, not a straight line. Because your cousin might have a third eye doesn’t mean that you’re not closely related to him. Tiktaalik is a few branches away from the line that eventually led to tetrapods. Thus, it is free to undergo small changes away from the tetrapod line. I’ll give another example. Just like the genus Australopithecus is very much related to modern apes but on a parallel track and are similar to them, so too can Tiktaalik tell us about tetrapod evolution but cannot be used to explain the direct lineage of every single homologous part of function to tetrapods. Tiktaalik can offer us a good glance at tetrapod evolution, but it cannot necessarily offer a step-by-step look in every single place. And because it did not lead directly to tetrapods, it can shift in subtle ways in its fins or other places. This is one of the basics of evolution.

    Fourth, I was only talking about Tiktaalik when I said that scientists could make predictions using evolution. It was found because scientists predicted a general window in which fish began to evolve toward tetrapods, not an exact date. What this new discovery does is push tetrapod evolution back several million years, which is nothing in evolutionary time, but it still comes within that general window in which tetrapod evolution could have occurred. We did not, on the other hand, find it at the deepest layers of the fossil record where it cannot belong. It came near the time when tetrapod evolution occurred. How this can be a strike against evolution is beyond me.

    Ecological zones cannot account for the fossil layers. Many groups of organisms appear in both older and later layers, while the opposite is not true: some organisms that we would expect to find earlier, like whales, appear later. Reptiles and amphibians also appear before mammals. These are what we’d expect given the order of evolution. We would also see ecological zones as general trends. Mammals would still appear earlier, for instance, if this was true. Lastly, you’d have to name actual misplaced fossils, which I assume is very similar to what I was asking for.

    You gave me a lot to look at with those links (then again, so did I), I will respond to them. The first link: I’m not going to speak for these scientists, but when scientists like Carroll talk about gaps, what they usually mean is that we don’t have a direct line of ancestry species to species. This kind of thing is incredibly misleading to quote without context because when people hear that, they think of it in terms of distinct groups that cannot be reconciled. But that is not true. There is an entire suborder of amphibians called Reptilimorph that are essentially reptile-like amphibians. Diadectomorpha, in fact, was once classified as a reptile but is now an amphibian, so it straddles the line. We do see a general transition in the fossils, but one problem is that the amnion, which reptiles have, does not really fossilize. Anyway, a short explanation of the transition is given here: http://www.all-about-reptiles.com/evolution-of-reptiles.html.

    So there are gaps, but to say that is to say that there are some groups that have traits which can be evolved into one other, which is the case here. I’ll get to this toward the end, but to even say a genus like Australopithecus has “precursor” features to genus Homo is to admit that the potential exists. In fact, at the end of the first section, the author falls into use of evolutionary terms like appearance in the fossil record. Even if two groups ostensibly appear simultaneously in the fossil record, which usually means a gap of at least a million years, it means that they evolved and then lived around the same time, which is what we would expect from evolution, not creationism. Under ecological zones, if I am understanding the use of the term, this would be a staggering coincidence.

    Furthermore, I question many of the author’s conclusions, for instance, that there are no links between pelycosaurs and theraspid. The author quotes a book from 1988, but in 1996 there was a paper examining tetraceratops as a very real possibility. In fact, there has been a debate about whether to classify tetraceratops as a pelycosaur or theraspid. Since we don’t have much to go by with tetraceratops, meaning that the fossil is hard to reconstruct, there is also biarmosuchia, which has a skull like some pelycosaurs but the temporal fenestra like a theraspid. And by theraspids appearing “simultaneously”, the author means millions of years. The upper Permian lasted 10 million years, and the first theraspids appeared in the middle Permian. Dinocephalia appeared in the middle Permian, for instance, and is somewhat related to biarmosuchia. Cynodont, a suborder that would later lead to mammals, has many subgroups linking it to other theraspids. There is the genus procynosuchus, which shows teeth and mouth structure diverging away from theraspids but still not at the point of later cynodonts. There is also the genus dvinia, which is somewhat similar to procynosuchus but diverges in places. These are from the upper Permian.

    In the step toward mammals, Hadrocodium, which was discovered in 2001 and got little fanfare, doesn’t give us a full picture of the mammalian ear evolution, but it does push our knowledge of the process farther back. It shows a late stage in the separation of ear bones from the jaw. Some of the bones have become part of the ear, for instance, but it retains a bay as if they were still part of the jaw. There is also Probainognathus, which has more reptile-like characteristics. You can read about both of them here: http://www.palaeos.com/Vertebrates/Units/Unit420/420.300.html. You can argue that there are still some gaps, but it’s no coincidence that organisms generally moving to mammal-like characteristics also have bones slowly rearranging themselves toward a mammal-like structure.

    I believe that the evolution of marsupials and monotremes is not well understood, although Eomaia, discovered in 2002, is a Eutheria on a path toward placentals but with many characteristics like that of marsupials and unlike those of placentals. Furthermore, we do have good understandings of other orders like carnivore, primates, and rodentia. I’ll get to some of these in a moment. Gaps in the fossil record are not a problem if the fossils we do see point the way toward the evolution of future organisms. I feel that the author ignores many good organisms and misrepresents a few, which is a common trend here. The author ends with a contradiction, quoting someone who says that mammal evolution is the most puzzling event ever, yet he says that it’s the most well-understand. Then again, why is he quoting someone from 1944?

    Next, the second article. I’ll pick this up where it’s relevant. The author says that the change of position in the nostril is contravened by the differences in cranial anatomy, but individual features often vary, even within species, especially since not every species may be a direct ancestor. Sure, the blowhole might not mean much if we see a general “transition” nowhere else, but what is important is long term trends which show an eventual change to the organism in question, and that is what we see. In the transition to whale, we see shorter necks, more flexible spines, loss of hip bones, the emergence of a thin lower jaw, and changes in teeth. To be more specific, the early pakicetid had the same sound transmission as mammals and had poor underwater hearing. A few million years later, a new species has developed something closer to the modern whale. This site http://www.edwardtbabinski.us/whales/evolution_of_whales/ is very in depth.

    Many whales have actual femurs and hip-joints. The article you linked to also calls them hind limbs, but let’s not get too far into semantics. The fact that bone remnants anchor the muscles of the genitalia is a good reason for vestigial qualities because there is no good reason to use them unless they were adapted for that purpose from ancestors with hind limbs who walked on land. The definition of a vestigial organ isn’t that it is useless, but that has begun to lose its original structure and function. For instance, a fish doesn’t have these bones because they never evolved from ancestors who had them. But whales have them because they evolved from mammals. Also, embryos in their incipient stages develop limbs much more like limbs used by ancient ancestors than anything that a whale has. They also develop other things like hair and olfactory lobes that they are not born with.

    This site http://www.palaeos.com/Vertebrates/Units/520Cetartiodactyla/520.120.html talks about the ankles of rodhocetus and the way that they were used for swimming. Why would we label this “just” like an otter when it clearly shows changes in structure toward what would become a whale? The ankle-bones are spooled, like artiodactyls, and it uses its limbs to swim. As the palaeos article points out, there are subtle differences by which it displaces water during a swim.

    The author quotes a paper from Thewissen and others in order to attempt to prove that whales didn’t evolve from pakicetids, and yet the entire point of the paper he quotes is to say that the whale’s land-based ancestry is obvious and clear. I don’t know if quote mining is going on or what, since I can’t access the paper, but you can verify it on Thewissen’s site: http://www.neoucom.edu/DEPTS/ANAT/Thewissen/whale_origins/index.html. “Pakicetids were the first cetaceans.” He says that they had an ear region similar only to whales and had teeth much like ancestral whales.

    The author fails to mention that the ear must undergo a lot of change in order to adapt to an aquatic lifestyle, so the evolution of the cetacean ear is interesting precisely because of the radical changes that it undergoes, not that it stays the same. The paper he cites talks about these “fundamental changes”. To quote the paper: “The phylogenetic evolution of cetaceans from a terrestrial ungulate ancestry is documented by an excellent fossil record. The relationships of the transitional groups are well resolved. Stepwise anatomical evolution through this transition is well established in the early fossil groups, in spite of the enormous anatomical differences between extant cetaceans and other extant ungulates.” In other words, the differences may be large, but we know how they evolved. It also says that all post-pakicetus cetaceans “share a large number of derived basicranial characteristics.” He then goes on to describe how these organisms evolved. http://deepblue.lib.umich.edu/bitstream/2027.42/48633/2/ID499.pdf It begins around page 79. The paper finishes by saying that it studied basicranial characters morphologically intermediate between land mammals and extant whales indicating the underwater hearing we associate with whales evolved gradually through a series of steps. And this is the author’s great source of refutation?

    Third article: You can call Homo habilis very much like Australopithecus, but it is still caught in a moment of “transition”. The face projects less. The teeth are smaller. Its brain size is larger, overlapping the area between Australopithecus and Homo erectus (which I will get to in a moment). To call it “just” an Australopithecus is wrong. The author constantly makes the mistake that such a divide means no connection altogether.

    In fact, Bernard Wood, the co-author of that paper, found that out of 11 features relating to cranium and mandibles, four of them – size of the mandible, brain size, parietal sagittal curvature, and molar crown size – were intermediate between Australopithecus and Homo erectus. Two others resembled Homo like features. Furthermore, of species like habilis and ergaster, Wood said that each demonstrates a significant and distinctive shift away from the Australopithecus adaptive plateau. This is all from the book Shaking the Tree. This is what happens when authors pick and choose data from evolutionists doing actual research.

    The brain size section seems disingenuous. Even if what Collard and Wood said is true, which is accepted uncritically by the author, that doesn’t invalidate all measures. In fact, Collard and Wood use their own estimate of brain size. So I believe that they are talking about adjusting the measurement, not invalidating all of them. They say, “…the relative brain size of Homo erectus is an intermediate between those of A. africanus and H. sapiens.” The author doesn’t reveal these full details.

    Lastly, I don’t know whether a gene can be found based on its location in other species, but a gene that looks like it will code for yolk could code for yolk (excepting its degraded base pairs). This can be known just by comparison. The original paper can be found here and lists it as the same general genes: http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0060063. Interestingly enough, monotremes have egg yolk genes that are stopgap between reptiles and later mammals down to their very genotype. I also know what creationists believe about pseudogenes, and I am loathe to get into an argument about it, but one would wonder why a creator would basically duplicate an egg yolk gene, riddle it with random errors, and then put it to work regulating (and I’m gonna need some proof that this gene does regulate). This makes sense under evolution, of course. Pseudogenes may be co-opted for functions at any time (although some pseudogenes just look too damaged to do anything at all, thus making them useless).

    The last few points I answered throughout the response.

  2. Jacob says:

    I hate to comment in an unrelated thread, but older threads seem to be closed after a time, and I had a long response prepared in the Ida thread. Can it be opened again, or can another thread be established?

    Since I’m posting, I might as well be on topic: actually, a lot of biologist for decades have been surmising possible functions for this DNA that we are now just discovering. In fact, if one were an ultra-adaptationist, one would predict that most DNA would have a function since it would be selected for. Here is Larry Moran’s response to an adaptionist:

    “Nobody is arguing that every single Alu element is junk. That would be stupid because we know for a fact that some of them have secondarily acquired a function. The point is whether most of this repetitive sequence can be reasonably assumed to be functional, and if so, what kind of function does the adaptationist imagine for most of these sequences?

    In the absence of any reasonable functional explanation, and in the face of evidence that most Alu elements are degenerate retrotransposons, it is reasonable to adopt the working hypothesis that they are junk. That’s not a science stopper. It’s just common sense.”

    Of course, it sounds like a response to a creationist, but it depends upon the methods of evolution. If one thinks of selection as some incredibly fine tuning element, then that’s one thing, but evolution is generally understood today to create a varying level of mistakes. It doesn’t matter how many functions Meyer lists because that’s not the point that people actually make (it’s ironic that one creationist I argued with actually used Ayala to support his position that pseudgenes are functional, while Meyer denigrates him for the opposite). Like Moran said, of course functions can be found, and it might look impressive to list them, but Meyer acts like these are common rules, and they are not. Some of them may be co-opted for functions, but that does not explain why many of them, even the functional ones, may sometimes be degenerate.

    Furthermore, you’re only quoting part of the ENCODE thing. For much of the DNA they looked at, they actually found no selective pressure, thus no selection for conservation, and the potential for that section of the DNA to fall into disrepute. They did find that a lot of DNA was transcribed, but there are also large parts that are not transcribed, which needs to be explained. There is also one study which showed that some RNA actually is “thrown away”. A quote from another researcher doing work on RNA, I’ll have to find it, but it was about how most RNA isn’t actually conserved and how it may just be genomic noise without function.

  3. jlwile says:

    Greg, lots of biologists don’t know about it, because biologists like Ayala make demonstrably false claims about it. Indeed, it seems only the creationists really understand junk DNA:

    http://www.trueorigin.org/pseudogenes01.asp
    http://www.godandscience.org/evolution/junkdna.html#hzRO7SiLbRE0
    http://www.grisda.org/origins/53007.pdf
    http://creation.com/images/pdfs/tj/j14_2/j14_2_18-30.pdf

    Evolutionists ought to start taking such points seriously, as they are steadily losing credibility on this issue.

    The reason some biologists make such demonstrably false claims about “junk DNA” is because the evidence for common ancestry is so poor that they have to try to come up with something:

    http://www.trueorigin.org/homology.asp
    http://origins.swau.edu/papers/evol/gibson/default.html

  4. jlwile says:

    Jacob, WordPress closes the threads after a certain amount of time. I am not sure how to open them again.

    In answer to Larry Moran’s question, OF COURSE it is reasonable to assume that all the Alu sequences are functional. First, some of them have been demonstrated to be functional, and the vast majority of them seem to be transcribed. Thus, it is actually going against common sense to think they aren’t functional.

    Meyer acts like the functions found for SINEs are general rules because they probably are. Once again, the fact that they are mostly transcribed indicates that functional SINEs are the general rule. You have to go against the science to assume otherwise.

    I think you need to read the ENCODE thing again, as I don’t think you understood it. You are correct that they found no selective pressure on some sections, but that does not mean no function. As they say, “However, the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution, at least when examined by current methods used by computational biologists. According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species’ genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction.” So the sections are functional, but their function doesn’t specifically pertain to survival or reproduction. Of course, the more reasonable conclusion is that they are not conserved because those functional elements NEED to be different in different creatures. Thus, those non-conserved elements are very species specific.

    You are absolutely WRONG that they found “large parts that are not transcribed.” Indeed, the scientific paper shows that 93% of the portion of the genome studied is transcribed. [Birney, E., et. al., "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project," Nature 447:799–816, 2007.] Thus, only a tiny fraction of the genome is not transcribed. This can easily be understood as deterioration of once-functional elements.

    Thus, I have clearly characterized the ENCODE results accurately. As they say, “The new data indicate the genome contains very little unused sequences…” (emphasis mine).

  5. jlwile says:

    Jacob, I don’t mind you dropping it in another post, since the comments are disabled on the relevant post.

    The Ida story has nothing to do with evolution per se. The fossil was repeatedly announced as something that will “change everything.” Now we know it adds little to the discussion. Thus, it has nothing to do with evolution. However, it does show us how irresponsibly evolution is communicated to the general public, and that (of course) was the clear point of the post.

    I don’t care to refute the Gallup poll, because it is not necessary. My point was that the number you gave as “real” is 1%. You can’t back up that number. Instead, you have to infer things from the Gallup poll and from the Discovery Institute’s list. Thus, unlike you claimed, the 1% is NOT a real number. Once again, evolutionists often claim things are “real” or “fact,” but further investigation shows that they are neither. This is, in fact, how most of the rest of your post can be characterized.

    No, you don’t get the point of the Luskin article or Gee’s comment. First, you claimed that evolution predicted where to look in the fossil record for a transitional form. Paleontologists looked there and found Tiktaalik. This was supposed to show that evolution can predict things and those predictions have been verified. In fact, the prediction was falsified, as the new fossil shows that they were looking in the wrong place.

    Of course I understand what you are saying. When evolution’s prediction that clear, straight-line lineages would be found in the fossil record was falsified, of course evolutionists had to come up with some way of “explaining around” the data. That’s why you only see branches now and no lineages. However, that doesn’t help your argument about Tiktaalik, because once again, it’s in the wrong place. It might, indeed, be some “cousin” to the actual transition, but that cousin hasn’t been found where it is supposed to be. Thus, the prediction you claimed was verified was, in fact, falsified.

    You claim that evolution provided a “general window,” but that general window was wrong. What you fail to understand is that even through the lens of evolution, Tiktaalik was A LONG WAY from a tetrapod. Thus, the date hasn’t been pushed back a small amount. The tracks indicate that full tetrapods were alive BEFORE something that was a LONG WAY from a tetrapod. Thus, the window must be pushed back a LONG way, and that’s why Gee says that “an enormous evolutionary void has opened beneath our feet.”

    You agree that there are gaps in supposed mammal evolution, and I agree that there are a few fossils that, with the appropriate imagination, could represent part of a progression from reptile to mammal. However, it is clearly not “a robust set of fossils for the evolution of mammals,” as you claimed in your post. That is my point. As the author of the article clearly shows, the fossils are a jumbled mix of many different animals that can only be seen as indicating evolution if you WANT them to.

    Whale evolution can be characterized in the same way. It is incorrect to say, “In the transition to whale, we see shorter necks, more flexible spines, loss of hip bones, the emergence of a thin lower jaw, and changes in teeth.” What we see are marine reptiles and marine mammals, each of which has fully functional structures for their ecological niches. You are also terribly incorrect to say, “The fact that bone remnants anchor the muscles of the genitalia is a good reason for vestigial qualities because there is no good reason to use them unless they were adapted for that purpose from ancestors with hind limbs who walked on land.” The bones do their job very well, so there is no reason to think they are there as a result of a loss of function. Instead, since they do their job so well, it is most scientifically reasonable to assume they are there SPECIFICALLY for that function and that it is a very good design.

    You ask “Why would we label this ‘just’ like an otter when it clearly shows changes in structure toward what would become a whale?” That’s not what the fossil shows. What the fossil shows is that, just as the link you gave said, the ankle is constructed to reduce the effects of water resistance during the recovery stroke. This is a great design and doesn’t at all indicate a change towards becoming a whale.

    I think you didn’t get what Woodmorappe was saying about the ear fossils. Basically, he says that the fossils we have supposedly showing the evolution of hearing in whales is just like the figure he constructed showing the evolutionary emergence of 18-wheeled trucks. Once again, if you WANT the fossils to show transition, they can (with a lot of imagination). However, the devil is in the details, and as you admit, those details are sorely lacking. If I can make a similar lineage out of things that clearly DIDN’T evolve, how is it that your lineage is evidence of evolution?

    To call Homo habilis “just” an Australopithecus is not wrong. In fact, it is the most reasonable interpretation of the fossils. You seem to think that all Australopithecines were very much the same, but like all creatures, there are ranges over which their features span. Homo habilis is so similar to Australopithecus that it makes sense to assume it is part of that range.

    The brain size section of that article is certainly not disingenuous. As he clearly says, the idea that brain size is related to intelligence just doesn’t square up with modern findings. The book Design of Life has a great discussion on that as well.

    It is also clearly wrong to say, “but a gene that looks like it will code for yolk could code for yolk.” That is not at all true. A gene’s function doesn’t depend on what it “looks like” it could code for. It depends on when it is activated, how often it is transcribed, and a whole bunch of other factors. It is also just plain silly to say, “but one would wonder why a creator would basically duplicate an egg yolk gene, riddle it with random errors, and then put it to work regulating.” There is no evidence that the gene is a yolk gene that is riddled with random errors. It has some similarities to the yolk gene, there is no question about it. However, that simply may give us some clues as to what its function is. To assume that it came from a yolk gene is not warranted by its structure. It is much more reasonable to assume it is a regulatory element.

  6. Greg says:

    It’s not just that your feeble attempts to deny the overwhelming evidence for common descent (I saw no responses to synteny or redundancy arguments anywhere there) aren’t worthy of consideration by secular biologists, there aren’t even taken seriously by qualified creation biologists;
    http://toddcwood.blogspot.com/2010/03/primer-on-transposable-elements.html
    http://toddcwood.blogspot.com/2010/03/more-on-transposable-elements.html

    Todd Wood wrote an entire research paper for creation biology in 2006 outlining all of the evidence for common descent and explaining why creationists’ responses, which largey involve ad hoc appeals to ‘common design’, fail. Why are you 4 years behind your own researchers?

    Whether certain unitary pseudogenes have picked up new functions is irrelevant. The whole point is that these were clearly previously performing a certain function and have now accumulated mutations preventing them from doing so. When we can see identical inactivating mutations, as in many cases, the evidence is only more compelling.

  7. Amanda Read says:

    I’m still amazed that Evolutionists are so confident that life could have started out simple and gained complex design through mutations. One guy sent me this video as “evidence of the chemical evolution of the cell,” or how life could have started without Creation: http://www.youtube.com/watch?v=U6QYDdgP9eg

    I couldn’t watch it with a straight face. The way they end as “it’s just chemistry…”

    ~Amanda~

  8. jlwile says:

    Greg, the only feeble attempt I am seeing here is the attempt to demonstrate common ancestry between different kinds of creatures. Todd Wood makes the same mistake most evolutionists do – he thinks his theological arguments (what would God do?) are more important than the data. I choose to follow what the data say, and the data clearly say that the vast majority of the genome has function.

    You can believe with as much fervent faith as you want that these functional genes “picked up new functions” over time, but once again, that is a belief that has no data to back it up. You NEED them to have picked up new functions in order for them to be consistent with the concept of common ancestry, so you believe it. I prefer to believe what the data say.

    Wood also makes some absurd claims. For example, he says, “Third, the argument for the common ancestry of chimps and humans depends in no way whatsoever on the functionality of transposable elements.” That is clearly false. If the element is functional, then it is consistent with the idea that it was designed. The fact that humans and apes share many genetic elements is not surprising in a creationist model. In fact, the creation model predicts it, because the genome is designed based on the needs of the organism, and humans share many needs with the apes.

    In his second post, Wood has to contradict his first post. He claimed in his first post that no creationist has dealt with TEs, and then in his second post he proceeds to summarize A LOT of creationist work on TEs. Of course, he doesn’t LIKE the conclusions, so he blithely dismisses what he once claimed didn’t exist with an absurd question, “Why have animals so similar to humans at all? Why not just make a world with humans and mammals but no primates at all?” For anyone who has a science education above that of a 9th-grader, the answer is patently obvious. Humans and other primates occupy different ecological niches, and THEY ARE ALL REQUIRED to balance ecosystems.

  9. jlwile says:

    Hi Amanda,

    The video is really funny. It makes a claim Shooter tried to make, that evolution and the origin of life are not connected. I showed Shooter the absurdity of that argument, and he had to eventually give up. I love some of the other nonsense in the movie, like the claim that it’s just MODERN cells that can’t be formed naturally. Surely, some mythical, mystical “primitive cell” could have been formed that way. Of course not, as even the simplest cell we can come up with is staggeringly complex. As The Design of Life and Life’s Solution make so clear, all the data we have show that abiogenesis just doesn’t work.

  10. Jacob says:

    I posted the first comment, but it did not seem to go through, even after a few hours. It still had not appeared when I posted the second comment, but it seems to be there now.

    As for non-coding DNA or junk DNA or whatever you want to call it: I did not say that conservation is the same as function. I said that they are free to fall into disrepute, but let me clarify: they are allowed to change freely. This supports the idea of genetic drift, which predicts that many elements are not adaptations but nevertheless do not cause great harm to the organism. I have actually heard creationists use the exact opposite argument that you make: that organisms may share parts of DNA because we are all based on the same blueprint. I suppose that some parts may need to be different, but that’s an odd argument. An omnipotent god isn’t exactly constrained by necessity (and before anyone says that creationism or ID doesn’t predict the nature of the creator, we all know what most of their constituents believe). It’s hard to see, anyway, why a salamander would need so much of its DNA. There is nothing so unique about it that it would flout every expectation that a designer would work efficiently (and a perfect designer working perfectly efficiently).

    By the way, the part where you stopped quoting is exactly where they begin their explanation: it may be used as a warehouse of natural selection. I kind of hate that term because it implies that things are being stored, whereas it is more likely that they just sit around with no purpose and then may be acted upon. And you still have to explain why many of them are accumulating errors.

    “Only” 7%? That 7% accounts for tens or hundreds of millions of base pairs. That, to me, is large, and it must also must be explained. And like I said, transcription may not mean anything. One paper http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4G9JKF1-C&_user=10&_coverDate=06%2F03%2F2005&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=e0429a4a50df049898e187f0c898b26d found this:

    “Surprisingly, however, RNAs originating from these regions are rapidly degraded by the combined action of the exosome and a new poly(A) polymerase activity that is defined by the Trf4 protein and one of two RNA binding proteins, Air1p or Air2p. We show that such a polyadenylation-assisted degradation mechanism is also responsible for the degradation of several Pol I and Pol III transcripts. Our data strongly support the existence of a posttranscriptional quality control mechanism limiting inappropriate expression of genetic information.”

    That’s in yeast, but another paper found that something similar may happen in humans. However, a lot still isn’t known (as Ryan Gregory said, we still should wait to determine the truth, but it’s also hard to prove a negative).

    Second post: It didn’t seem like much of a concern post to me. It seemed to be making broad generalizations. Actually, the original paper on Ida, rather than based on “fervent faith”, was based on a lot of evidence, but it was extremely hasty in its claims. Many scientists tore it apart immediately, and a few months later it was reexamined. The mistake was corrected. The claim you made doesn’t even make much sense. Why does it take a faith in anything to draw the conclusions that they did? If it turned out to be what it is now, then it fits right in with previous knowledge, like most fossils tend to do. But if it was an unknown “transitional” (I hate using that term because it implies that everything about the organism like with Tiktaalik must be caught perfectly between two different states), then the creationists would still deny evolution. Either way, it doesn’t affect belief in evolution or the veracity of it. It just expands on the evolution of a certain clade.

    What I said about that number was that it was a real figure. If you count 20 red marbles out of 100, then you have 20%. There are a certain number of scientists who claim to be creationists. There are a certain number of scientists. That to me sounds like we can arrive at a good estimate. However, this is not a science, so stop conflating the two. I did not say that it was accurate down to the last man, but neither are polls. Even they have a margin of error. And it’s tough to disparage me when you uncritically accept the idea that scientists are abanonding evolution without any proof.

    Shubin was, of course, right to predict Tiktaalik. He was able to predict something very much like it in the first place based on how we believe that things evolve (whereas, creationism has no predictive power when it comes to what organisms should generally exist). No matter what was recently found, a Tiktaalik-like creature still existed. That is fact. The only question is whether he could have looked back another 20 to 30 million years and found something similar. Maybe it’s just me, but it’s impressive that even with this monumental shakeup, Shubin was only off by about half or one percent of all of the time since the beginning of the Earth. Yes, I’m aware of the time difference. The tracks are like Ichthyostega, so we’ll probably have to turn things back another 40 million years at the least. But why 40 million? Why not 100 million? Or 500 million? Proto-tetrapods could exist anywhere. We could have found them in the Proterozoic, thus destroying evolutionary theory completely. Do you think that it’s the biggest coincidence ever that most of these proto-tetrapods are appearing in this small, one percent window? Even if we consider nothing else, I say that it’s too big of a coincidence. Evolutionary theory is the only thing I know of that can account for that, so while ammendments need to be made, it stands strong. Now, a Tiktaalik with wings (and no explanation for them) would falsify. Tiktaalik in the Cambrian would falsify. But there is nothing about this new discovery that says that it is not possible according to evolutionary theory.

    Also, one needs to consider that most discoveries are based on previous discoveries (Ichthyostega was one of the first discoveries, so we’ve been attempting to work backwards from there). Now that new information has come in, a whole new avenue has opened up, allowing us to find things that we necessarily did not consider, although I believe that the tracks were found in an area where things did not fossilize well, but I wouldn’t doubt it if new discoveries are eventually forthcoming.

    You didn’t answer anything about ecological zones, I believe. If no answer is provided, then according to creationism fossils should be randomly assorted, which is definitely not what we see.

    I believe that it was Darwin who originally invoked the idea of a tree of life, and maybe some before him, but it doesn’t matter. The whole point of science is to amend and reach better conclusions. The “tree of life” is only incorported into the theory of evolution because it fits with the evidence, which is a virtue, so I’m not sure what the point here is.

    Of course there are gaps. If we really wanted to chart how evolution worked, we could hypothetically chart the mutations that happen across every organisms throughout time, but I think that most people would be happy to see evolution charted through a member from each species. However, we don’t even need that much. If we see somebody traveling north along one street and then ten minutes later west along another, then we can assume that they turned left (or at least took a convulated path there, which is actually a good analogy for evolution).

    And we have more than a “few” turns (or fossils) to demonstrate this. In the Reptiliomorpha (again, reptile-like amphibian) superorder alone, there are four (possibly five) different orders, at least 16 different families, and (by a rough estimate) probably at least 40 or 50 different genera and species. Proterogyrinus scheeleri, Solenodonsaurus janenschi, and Hylonomus lyelli (one of the first known reptiles) are just a few species that had varying levels of “intermediate” characterstics. The latter, which was technically a reptile, had a skull, shoulder, pelvis, and limbs closer to an amphibian, the rest of skeleton and jaws closer to a reptile, and verebraeand teeth somewhere in between.

    Pelycosaur to therapsid: so far there are about 13 or 14 separate genera of biarmosuchia (the dinocephalia,which was a therapsid but nevertheless had no secondary palate and had dentary like the pelycosaur, had over a dozen different genera so far known). You can read about the suborder here: http://www.palaeos.com/Vertebrates/Units/400Therapsida/200.html If you go back a little further, then there’s Sphenacodontoidea, which contains about four or five separate genera. Anyway, I could go on, but for now I’ll link here http://www.talkorigins.org/faqs/faq-transitional/part1b.html because it has some very in-depth explanations. For instance:

    “Procynosuchus (latest Permian) — The first known cynodont — a famous group of very mammal-like therapsid reptiles, sometimes considered to be the first mammals. Probably arose from the therocephalians, judging from the distinctive secondary palate and numerous other skull characters. Enormous temporal fossae for very strong jaw muscles, formed by just one of the reptilian jaw muscles, which has now become the mammalian masseter. The large fossae is now bounded only by the thin zygomatic arch (cheekbone to you & me). Secondary palate now composed mainly of palatine bones (mammalian), rather than vomers and maxilla as in older forms; it’s still only a partial bony palate (completed in life with soft tissue). Lower incisor teeth was reduced to four (per side), instead of the previous six (early mammals had three). Dentary now is 3/4 of lower jaw; the other bones are now a small complex near the jaw hinge. Jaw hinge still reptilian. Vertebral column starts to look mammalian: first two vertebrae modified for head movements, and lumbar vertebrae start to lose ribs, the first sign of functional division into thoracic and lumbar regions. Scapula beginning to change shape. Further enlargement of the ilium and reduction of the pubis in the hip. A diaphragm may have been present.”

    It’s possible that they could be wrong, but just don’t sell them short with vague refutations. You keep saying that these creatures don’t fit within an evolutionary framework. Explain why, because these details seem pretty clear and in-depth to me.

    Whale evolution: Of course the Ambulocetus seems well-adapted. Each form is probably going to be well-adapted at a different stage along the path back to the ocean. However, your argument would only be relevant if we have absolutely no idea how an organism can slowly become more acclimated to the water. Fortunately, we have several different organisms, each using various methods (in fact, most living organisms that can both swim and walk use different methods). For instance, Rodhocetus had smaller hind limbs (Basilosaurus and Prozeuglodon had shorter and shorter hind limbs too) and a shorter femur than Ambulocetus, but it had a more complete tail vertebrae. Its nostril was also beginning to move back. By admitting that there is a huge gradient of different ways in which to swim, then you admit that hypothetically an evolutionary pathway could be found from one to the other, each one adapting a slightly different and subtle method along the way. As its legs become reduced, maybe it begins to use its tail more and its forelimbs begin to change.

    Of course the pelvis or hip bones work well for the whale. Evolution obviates the necessity for design. However, that’s not the point. There is no reason why whales need femurs, but evolution answers that. It answers why whale embryos are rife with all of the unnecessary genetic baggage from their land-based ancestral past. It answers why certain whales have a 1 mm auditory meatus and muscles for external ears. Is it just a coincidence that all of these look like lost or blunted traits from mammals?

    Unless you can literally see every single organisms that led from one species to another, you can always say that each is a separate species distinct from the other. That’s a useless statement in and of itself. However, it’s hard to deny the changes we see in organisms throughout time. Yes, I get the point of the author’s comparison. I have heard it many times. However, he is banking on the silly coincidence that not only do whales appear around the time of mammals in the fossil record, they also appear around the time of these “proto-whales”. His analogy is wrong, anyway. If that 18-wheel truck still has unicycle parts sticking out of it, then maybe I can conclude that it is a modified unicycle (very, very heavily modified).

    For every characteristic I bring up, all you can offer is a vague claim that barely functions as a refutation. The point, I believe, is to prove what we’re saying. The author is just picking and choosing what he wants when he quotes a researcher who clearly said that out of 11 characteristics he observed from habilis, over half were either intermediates or homo related. And if you say that there is variation within classifications, then you admit that organisms can exist on either end of the bound, which contravenes the entire idea that they’re totally separate.

    I’m pretty sure that researchers can tell genes apart by their location. From the paper: “Interestingly, by using highly sensitive similarity search algorithms, we identified a few VIT pseudogenic coding sequence remnants (mainly from VIT1 and VIT3) with premature stop codons and frame-shifting insertion/deletions (indels) in regions syntenic to those containing these VIT genes in chicken.” I’m not sure if they mean totally homologous places or just within the same chromosome. However, later they say that VIT remnants are true VIT sequences. Furthermore, I don’t know if this gene fully transcribes, but not all of them do, so you can’t just hold out hopes for a function in all of them.

  11. No, my point was that the origin of life is not understood. You take that as evidence of the impossibility for natural processes to create life, whereas I will wait to see how life got started before I say it couldn’t have happened naturally.

    And do not take having the last word as evidence of me giving up. If you do, then you’ll have to admit that you gave up on this post.

  12. jlwile says:

    Jacob, when you say, “It’s hard to see, anyway, why a salamander would need so much of its DNA” you are only demonstrating that we know very little about genetics. You might think it is hard to see why a salamander would need so much of its DNA, but I don’t. It takes an ENORMOUS amount of information to construct and sustain an organism. The amazing thing about DNA is how so much information is contained in so small a space. Thus, it is an amazing feat of design that DNA can hold so MUCH information.

    You say, “And you still have to explain why many of them are accumulating errors,” but you are ASSUMING they are errors. You see a change in a genetic element that you assume has no use and call them “errors.” A more reasonable genetic interpretation is that the changes are necessary for species-specific functions.

    You can ASSUME that transcription means nothing, but it is certainly not a reasonable assumption. There is a huge amount of energy devoted to transcription. To assume that all that energy is wasted is not consistent with what we know about the incredible efficiency of life. The paper you cite doesn’t even suggest this. It simply says that the RNAs from the transcription of “supposedly silent intergenic regions” are rapidly degraded. As the authors indicate, this merely suggests “existence of a posttranscriptional quality control mechanism limiting inappropriate expression of genetic information.” Those RNAs, since they are transcribed, most likely have a function. However, once their function is rapidly completed, they need to be degraded in order to avoid further inappropriate action. Since you WANT to believe transcription doesn’t imply function, you are FORCED to believe that since the RNAs are degraded, they don’t do anything. There is no evidence to support that.

    7% is a tiny fraction of the genome, and as I said, the loss of 7% of a genome’s function can be easily understood in terms of mutational degradation. The problem is that you need to explain why so much of the genome that evolutionists have continually called “junk” and tried to use as evidence for common ancestry is actually functional.

    I agree that NOW we know Ida doesn’t affect belief in evolution, because we now know that contrary to the claims that were made, it adds little information to our knowledge. That was, in fact, one of the points of the previous post. We were confidently told that Ida would “change everything” when it came to our knowledge of evolution. Now we know it did no such thing, but no one is trumpeting that scientific result. Thus, the template remains – when something supposedly supports evolution, trumpet it. When further analysis shows no such report, don’t trumpet that analysis. Why was the paper on Ida “hasty in its claims”? Because the authors allowed their faith to interfere with the data.

    You said your 1% number was “real.” We now know you cannot support it in any way, which means it is not real. Nevertheless, you still defend your statement that it is “real” within some margin of error. It is not, in any way, real, which is demonstrated by the fact that you cannot support it. However, I can support the fact that scientists are abandoning evolution. The list of 700 scientists who are willing to risk their careers to state that they don’t think random mutation and natural selection can account for the complexity of life just keeps growing. Thus, scientists are leaving evolution, and their numbers just keep growing.

    If you interpret geology in terms of an evolutionary view, the tracks that you say are Ichthyostega-like appear roughly 40 million years too early. There are no known Tiktaalik-like fossils in the rocks that are 40 million years younger. Thus, Tiktaalik is in the wrong place. You can have faith that at some point, Tiktaalik-like fossils will be found in the “right” place, but you certainly can’t use the fact that they are in the wrong place to claim that a prediction of evolution was verified! It’s just the opposite.

    Of course, the more reasonable interpretation of the fossil record is according to a Flood model. In that model, the layers represent ecosystems, not ages. As a result, we expect organisms that are adapted to live in shore or shore-like ecosystems to be fossilized together. Thus, we don’t expect proto-tetrapod fossils to exist anywhere. We expect them to be grouped with other amphibian-like fossils, which is what we see.

    You keep saying that something like a “rabbit in the cambrian” or a “Tiktaalik in the Cambrian” would falsify evolution, but it certainly would not. The fossils would be dismissed as “stratigraphic leaks.” You claim that a “Tiktaalik with wings” (and no explanation for it) would falsify evolution, but a mammal with a duck’s bill (and no explanation for it) did not. All you say is that the evolution of the platypus is “not well understood.” Evolutionists will never accept falsification of evolution. Instead, they will simply ASSUME evolution and say that all conflicting data are “not well understood.” You can’t even accept that the tetrapod-like fossils 40 million years too early don’t falsify a specific prediction of evolution! Of course you won’t accept the data that falsify the entire hypothesis.

    I did, indeed, answer your question about how creationism expects fossils to be arranged. They expect fossils to be arranged according to the different stages of the Flood, and that’s exactly what the data show.

    The point to the “tree of life” is that fossils certainly don’t show it. Instead, they show the “orchard of life” that creationists expect – kinds that are separate and variation only within those kinds.

    “If we see somebody traveling north along one street and then ten minutes later west along another, then we can assume that they turned left (or at least took a convulated path there, which is actually a good analogy for evolution).” Once again, you think that the ONLY explanation that could be right is the one you WANT to believe. If you see somebody traveling north along one street and then ten minutes later west along another, it could be that it isn’t even the same person. It could be a twin, a relative, or just someone who looks like the other person. A real scientist would not exclude the other possibilities just because he doesn’t care to imagine them.

    I think you need to do some reading from some sources more reputable than the incredibly deceptive talkorigins site. Their “FAQ” on transitional fossils is far from accurate. For example, it claims “Scutosaurus and other pareiasaurs (mid-Permian) — Large bulky herbivorous reptiles with turtle-like skull features. Several genera had bony plates in the skin, possibly the first signs of a turtle shell.” Of course that is nonsense. The bony plates on Scutosaurus have nothing to do with turtle shells.

    Of course, the big thing the FAQ conveniently leaves out when it comes to turtles is that the evolution of the turtle shell is so poorly-documented that evolutionists can’t even tell whether or not a new fossil is an ANCESTOR or DESCENDANT of modern turtles.

    Its list of transitions from synapsid reptiles to mammals has been shown to be more the product of evolutionary imagination than data by the article I have already linked to you, which you couldn’t refute. All you could do is offer the vague refutations you accuse me of offering.

    Once again, your interpretation of whale evolution is the result of imagination, not data. You say, “Rodhocetus had smaller hind limbs (Basilosaurus and Prozeuglodon had shorter and shorter hind limbs too) and a shorter femur than Ambulocetus, but it had a more complete tail vertebrae. Its nostril was also beginning to move back.” You are right that Rodhocetus had smaller hind limbs and Basilosaurus had even shorter hind limbs, but that doesn’t imply transition between the two. It indicates that they had different NEEDS in terms of their hind limbs. A European wall lizard, for example, has long limbs. The Madrean alligator lizard has short limbs. However, no evolutionist claims that these two lizards are in the evolutionary line of snakes. The limb size is simply reflective of the ecological niche of each reptile. In addition, To say that the nostril was “beginning to move back” is also simply expressing your desire to believe what happened. In marine animals, there is a wide range of where the nostrils can be. Once again, their nostrils were where they NEEDED to be.

    You go back to your old mistakes with genetics when you say, “There is no reason why whales need femurs.” Of course there is a reason they need femurs. They need them to anchor and support the genetalia. You ask, “Is it just a coincidence that all of these look like lost or blunted traits from mammals?” No, of course not. It is a consequence of their FUNCTION.

    You say, “However, it’s hard to deny the changes we see in organisms throughout time. ” I don’t disagree with that. However, what you do is IMAGINE changes by viewing a fossil record. Changes do occur to a limited extent, and the limit is based on the organism’s genome. However, to claim that the fossils in the supposed evolutionary history of whales demonstrates that a land mammal gave rise to whales is most wishful thinking. It is certainly not what the data say.

    You say, “For every characteristic I bring up, all you can offer is a vague claim that barely functions as a refutation.” This, of course, is not true. I give you detailed articles, which you cannot refute. I give you facts that show your claims to be false, but you simply ignore those facts.

    You say, “And if you say that there is variation within classifications, then you admit that organisms can exist on either end of the bound, which contravenes the entire idea that they’re totally separate.” No, that certainly does not. There is a lot of variation within a created kind, but there is a hard wall that limits how far the variation can go.

    You say, “Furthermore, I don’t know if this gene fully transcribes, but not all of them do, so you can’t just hold out hopes for a function in all of them.” I don’t. However, I hold to what the data clearly say, which is that the vast majority of them have function. Some genes have probably lost function over time due to mutation, but the ENCODE results show that the vast majority of the genome has function. This goes counter to what evolutionists have both predicted and confidently asserted over the years.

  13. jlwile says:

    Shooter, your point is that you WANT the evolution of life to be not understood. That’s better than admitting what every origin-of-life experiment shows – it is just not possible in a naturalistic paradigm.

    Sorry, you can claim that I gave up on the last post, but I clearly didn’t. I corrected your mistakes, as I am happy to do. Of course, since you make so many errors, it is possible I have overlooked one or two. Which one did I overlook? Even though I doubt you will learn from the corrections, at least others might.

home | top