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Aron Ra vs Bob Dutko

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Aron Ra vs Bob Dutko
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australopithecusLime TordUser avatarPosts: 4347Joined: Sun Feb 22, 2009 9:27 pmLocation: Kernow Gender: Time Lord

Post Re: Aron Ra vs Bob Dutko

BobEnyart wrote:Even Richard Dawkins repeats that biology is the study of organisms that seem to have been designed, and LIKEWISE many atheistic physicists struggle to account for the apparent fine-tuning of the universe. So, as you say that God is hiding, many others, myself included, respond by saying that if so, He is hiding in plain sight.


1) Seems to be =/= how it is.
2) You don't know what fine tuning means in the context of physics.

AndromedasWake wrote:In physics, fine tuning is an undesirable consequence of being unable to explain variables which must be precisely set to make the model accurately describe the observable Universe. When something has to be finely tuned by a physicist, the immediate question is, "why should that be exactly right?"

If the physicist has an answer, then there is no fine tuning problem, because the mechanism for the given outcome has been established. Out-standing fine tuning problems indicate which parts of a particular model need work. Fine tuning is not the same as the speculative term "fine tuned Universe". This term is used to discuss the extent to which seemingly fundamental parameters in nature must take very precise values in order for us to be here. For example, in the standard model of particle physics, there are several values which, if changed even a tiny amount, would forbid any kind of higher chemistry to take place. Because fine tuning is a classical term which describes the action of a physicist (i.e. a person) the term "fine tuned Universe" has unwelcome connotations.

Linguistically speaking, it may imply that a person has set the natural laws which govern the Universe, and so is often used underhandedly by apologists such as William Lane Craig. He has used the phrase "the fine tuning of the Universe" thus merging "fine tuning" and "fine tuned Universe" together. The former describes intelligent action by its definition, the latter is an unfortunate overlap that would be better replaced with the word "precision" to avoid confusion. On pragmatic grounds, scientists must assume the precise values are a physical necessity if they are to uncover the process which relates them. William Lane Craig dismisses this on the basis that the values are "just arbitrary". This is where he exposes his inability to distinguish a model (a map) from reality. These values are arbitrary in their respective models, which is why they represent fine tuning problems. Thus they are also indicators of the incompleteness of their respective models. The apologist's perspective is that the models must already be 100% accurate, meaning out-standing fine tuning problems indicate a fine tuning of reality. No scientist puts so much faith into the current state of physics!
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Fri Dec 07, 2012 6:57 pm
BobEnyartUser avatarPosts: 45Joined: Sat Jan 28, 2012 2:19 amLocation: Denver, Colorado, USA Gender: Male

Post Re: Aron Ra vs Bob Dutko

nemesiss wrote:Dear mr Enyart,
your excessive agressive position against evolution, given the points you've provided, i would say are poorly based.
to keep it simple and direct, point by point:

- Universe and Galaxy recent creation observations astronomy
- Stars and Planets recent creation observations astronomy
- Physics and Geochronology physhics and geology
- National Parks correcting old-earth-biased signs geology
- Earth's Rapid Topographical Changes claimed to require millions of years. geology
- Genomes and Earth History biology and geology
- Dinosaur soft tissue biology
- Dinosaur Layer Biological Material geology? and biology

as pointed out by me, with the red text, none of these points are about evolution.

nemesiss, I believe that Gnug and James had both separately and specifically asked me how our discussion relates to a young earth, and so I pointed out that nonconforming sequences are part of multiple lines of evidence that undermine the Darwinist/old-earth worldview. That's it. I was answering their question. Regardless though, I think you would agree, if there is evidence that the Sun, stars, galaxies, are not billions of years old, as at that site, then that evidence would have great bearing on Darwin's theory. That's virtually a tautology. Agreed?

Thanks for asking,

-Bob Enyart
http://kgov.com/science
Taking on all atheists over at rsr.org/atheists.
Last edited by BobEnyart on Fri Dec 07, 2012 7:09 pm, edited 1 time in total.
Fri Dec 07, 2012 6:59 pm
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australopithecusLime TordUser avatarPosts: 4347Joined: Sun Feb 22, 2009 9:27 pmLocation: Kernow Gender: Time Lord

Post Re: Aron Ra vs Bob Dutko

BobEnyart wrote:nemesis, I believe that Gnug and James had both separately and specifically asked me how our discussion relates to a young earth, and so I pointed out that nonconforming sequences are part of multiple lines of evidence that undermine the Darwinist/old-earth worldview.


Except they don't undermine evolution, the article you're misunderstanding explains as such. It also gives an explanation for genetic anomalies, however you've dismissed that explanation because you don't understand the subject you're trying to refute and you don't understand the article or the science behind it.

When I pointed this out to you you decided you didn't want to continue with the discussion, and when I pressed you to admit you were wrong you decided, as you still are, to childishly ignore me for arbitrary, indefensible immature reasons. You assert we have no concession policy; you've demonstrated you have none yourself. Choosing to outright and dishonestly ignore others.

That's it. I was answering their question. Regardless though, I think you would agree, if there is evidence that the Sun, stars, galaxies, are not billions of years old, as at that site, then that evidence would have great bearing on Darwin's theory. That's virtually a tautology. Agreed?


There is no such evidence, outside of your inability to understand the subjects you seek to refute. You've demonstrated you know bugger all about biology, is this where you show us you know bugger all about physics too?
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Fri Dec 07, 2012 7:08 pm
nemesissUser avatarPosts: 1259Joined: Sun Sep 13, 2009 7:29 pm

Post Re: Aron Ra vs Bob Dutko

BobEnyart wrote:
nemesiss wrote:Dear mr Enyart,
your excessive agressive position against evolution, given the points you've provided, i would say are poorly based.
to keep it simple and direct, point by point:

- Universe and Galaxy recent creation observations astronomy
- Stars and Planets recent creation observations astronomy
- Physics and Geochronology physhics and geology
- National Parks correcting old-earth-biased signs geology
- Earth's Rapid Topographical Changes claimed to require millions of years. geology
- Genomes and Earth History biology and geology
- Dinosaur soft tissue biology
- Dinosaur Layer Biological Material geology? and biology

as pointed out by me, with the red text, none of these points are about evolution.

nemesiss, I believe that Gnug and James had both separately and specifically asked me how our discussion relates to a young earth, and so I pointed out that nonconforming sequences are part of multiple lines of evidence that undermine the Darwinist/old-earth worldview. That's it. I was answering their question. Regardless though, I think you would agree, if there is evidence that the Sun, stars, galaxies, are not billions of years old, as at that site, then that evidence would have great bearing on Darwin's theory. That's virtually a tautology. Agreed?

Thanks for asking,

-Bob Enyart
http://kgov.com/science


if this is a discussion on the age of planet earth, then the following points your points have no place om the discussion, for they create 'white noise';
- Genomes and Earth History
- Dinosaur soft tissue
- Dinosaur Layer Biological Material
- National Parks correcting old-earth-biased signs

if i take your statement serious, apart from evolution (which is an explenation for the diversity of life), Darwin also had another theory with regards to the age of the sun, stars and galaxies? i have to say i'm sorry, but that's just wrong.
an old-earth worldview existed long before CharlesDarwin, even prior to the calculation of the geneology in the bible.

the age of our planet has little value to the theory of evolution. evolution in itself is a very simplistic proces, that happens to have been taking place for more then a billion years on planet earth and is STILL taking place. the proces itself doesn't take billion of years, at it's smallest it takes perhaps only a microsecond, at a time. EVEN if it were so, that we were unable to find ANY animal remnants (be it fossil or not) that was older then 6000 years old, evolution would still be true.
that the processes that are responsible for formation of planets, stars and/or galaxies look quite similar to evolution is one thing, that does not mean they are the same. hence why some feel the need to say Biological evolution.

since i do not understand which definition of tautology you are using in this sentence, let me be as clear as possible:
Nemesiss wrote:The age of the earth, be it young or old, has NO bearing on the theory of evolution.
Fri Dec 07, 2012 11:38 pm
Gnug215ModeratorUser avatarPosts: 2688Joined: Sat Feb 21, 2009 10:31 pm

Post Re: Aron Ra vs Bob Dutko

BobEnyart wrote:
Gnug215 wrote:More small-time hole-poking, really.


Wow, that's all small-time hole poking? At least you'd have to agree, I would think, that the nonconforming sequences are not primarily limited to single-celled bacteria and the odd gene here and there. And if you agree with that, then you're agreeing (even if it's hard to admit) that Aron & Coyne are wrong in their assessment of the state of the art genetic analysis of the patterns of life. And if you can see that, then you should ask, why are they so resistant (as they are to seeing function in the decreasing list of human vestigial organs, and function in the alleged "junk DNA", which Darwinist prediction turned out to be the single greatest identified impediment to progress in genetics by mainstream scientists).


For my untrained eye, yeah, that sounds like small-time hole poking. I'm really, REALLY untrained in this. I haven't had biology since like... 7th grade.

I don't even know what Aron and Coyne said.


BobEnyart wrote:
Gnug215 wrote:And well, the thing is... whenever I see claims like these, someone always comes along and gives a - to me - perfectly logical explanation to these things. Or they come in and show you (or whoever the creationist making the claim is) wrong, somehow. Or... and I actually like this one... they say that they've discovered this weird new thing which was surprising, and they need to rethink their position, look at evidence again, test new things, etc. I never really see that in creationists, I'm afraid.


Gnug, I don't know you, so if this is wrong, I'll take you at your word. But if you think that creation scientists don't rethink their theories, challenge them with new observations, debate, etc., that must be because you haven't been reading the creation journals. And I think you will admit, that while evolutionists do all that debating and reassessing, that's all limited to refinements to their primary commitment to Darwinism (not to the question of whether or not molecules-to-man evolution is a fact), and that this is the same for biblical creationists, that while they debate the particulars, that is limited to refinements to their understanding that you didn't evolve from bugs but that God made you in His image. So, unless you acknowledge that your criticism directly applies to both camps, your objection appears to be arbitrary.


My pneumonia-ridden mind didn't do a good job here. I'll try to clarify:

I honestly never have seen creationists go back on their theories. I haven't been reading creation journals. Or any journals. But I do see it in science a lot, and there is a kind of humility and integrity about it that I just don't see in creationists.
I'm sure many of them have a prior commitment to "Darwinism", it doesn't seem to close to the prior commitment creationists have to God.

My criticism CAN (and does) apply to both sides, but I pretty much only see transgressions on the creationist side. It is perhaps not a wonder, either, when so many creationists that I see (I don't read a lot of journals, but I have watched a number of videos in my time) pretty much hold sermons about God and creation, with science as a kind of secondary theme.

You may not agree with him, but I will forever remember Ken Ham and his "Biblical Glasses". He's made an indelible impression on me. (Not a good one, as I'm sure you can tell.)


BobEnyart wrote:
Gnug215 wrote:I don't really believe in this atheistic bias that you speak of, not in the press, and nor in the scientific establishment... any scientist would love to be the one to make a new and startling discovery.


Many people don't like being called fools, morons, etc., by leaders in their field, as theoretical physicist Lawrence Krauss (emphasis on the theoretical) called the scientists whom I mentioned from http://cosmologystatement.org, "400 nuts." Scientists are people too. And science historians have filled volumes showing that scientific prejudices and bigotry are (sadly, but expectedly) alive and well.


Yes, scientists are people, too. Which is exactly why I'd expect any "truth" to come out of that establishment. The conspiracies that so many of your peers are so fond of expounding are simply not there. Such accusations really seem like the last refuge of desperate mind, so that's another problem for creationists in my eyes.
I am quite aware of the existence of bias, and I know it exists on both sides. The fact that a truth should be obvious to all, but isn't, is not something I put down to mental instability, lack of intelligence, divine intervention, lack of divine intervention, satanic intervention, or whatever charge either side will make about the inner workings of proponents on the other side. I think it is "simply" a matter of psychology - not psychological instability, psychological illness or the like - just "regular" psychological states of humans.

While this immediately exonorates both sides from a lot of things, I think it leaves the creationist side with one problem: the fact that God is letting it happen.


BobEnyart wrote:
[Something something... Lord Kelvin...]

I have to say, this whole thing about Kelvin, Newton and so on, is really one of those useless hypothetical conversations that leads nowhere. I think you and Aron were silly to engage in it in the first place. :(

What a bunch of dead guys would feel if they were transported to the present (and well, revived, obviously) is quite unknowable, and totally irrelevant, since the convictions of these individuals doesn't really count for anything.

Both side really need to let of this one. Debating whether Einstein believed in God, or whether Hitler was a Darwinian is so enormously pointless, it literally makes me sad to look at.


BobEnyart wrote:So Gnug, what seems to you that God is hiding is not how countless others perceive it. Even Richard Dawkins repeats that biology is the study of organisms that seem to have been designed, and LIKEWISE many atheistic physicists struggle to account for the apparent fine-tuning of the universe. So, as you say that God is hiding, many others, myself included, respond by saying that if so, He is hiding in plain sight.

-Bob Enyart
http://KGOV.com/science


Yes, whether God is hiding or not is a matter of perception.

For every seemingly organism that seems designed, and every universe-controlling feature that seems fine-tuned, the world displays so many odd and random things.
The fact of the matter is still that the number of explanations for natural phenomena that God stood for has been steadily falling throughout history, and the ones that nature itself stood for.

(I love how YouTuber NephilimFree suggested, nay, inSISted that the discovery of the above-expected spin of galaxies was the "Finger of God", as he triumphantly wiggled his index finger at the video camera. I'll make a bold prediction here that it won't be too many decades before we understand pretty well what's going on. I will also predict that NephilimFree will not recant.)

Well, according to you, God is hiding in plain sight. I disagree, of course. But if he is hiding in plain sight... why is he hiding at all?
I know that eternal debate about faith in the things not seen, but why should he hide, and yet still somehow make himself obvious to the world? That goes contrary to the point of us having faith in him in spite of not seeing him. It all just sounds like a really poorly executed test.
- Gnug215

YouTube channel:
http://www.youtube.com/user/Gnug215


The horse is a ferocious predator.
Fri Dec 07, 2012 11:49 pm
InfernoContributorUser avatarPosts: 2298Joined: Thu Apr 30, 2009 7:36 pmLocation: Vienna, Austria Gender: Cake

Post Re: Aron Ra vs Bob Dutko

I only want to give one answer to the many points raised here, because it's quite an extensive one. In the light of recent scientific advances, it's also a very important clarification, one that is almost universally misunderstood. I am talking, of course, about "Junk DNA".

Bob Enyart wrote:JUNK: I say to famed PhD anti-creationist Eugenie Scott in 1997 on national TV regarding her "Junk DNA" claim against creation (which was shared by virtually the ENTIRE Darwin community) that as genetic science advances, we're likely to learn that those billions of nucleotides that they claimed affirmatively had no function actually had function that we were still to discover. She disagreed, and now Nature 2012 publishes results from 440 researchers that 80% of the human genome has function, with the project lead predicting that will go to about 100% (which is undeniably, at least, the general direction of the trend).


Bob, the problem here is not what scientists have claimed and then found, but rather what the popular press has (mis)understood. This is also a story about scientists failing to communicate science properly. AronRa said on the 31st of May, 2009, in his video Ida Know (the first of a five-part summary about the 47-million year old primate fossil Ida) the following, which also holds true about this story:

But sadly, the media isn't entirely to blame, some of this has been done by scientists.

...

It is highly inappropriate sensationalism and the way it's described is very misleading to anybody who doesn't understand taxonomy very well and almost nobody does.


The same is true in this case, only substitute "taxonomy" with "evolution", "genetics" and "biochemistry".
A pop-science journal Arstechnica (Author John Timmer) has also commented on this phenomenon:

Most of what you read was wrong: how press releases rewrote scientific history wrote:Many press reports that resulted [from the ENCODE release] painted an entirely fictitious history of biology's past, along with a misleading picture of its present. As a result, the public that relied on those press reports now has a completely mistaken view of our current state of knowledge (this happens to be the exact opposite of what journalism is intended to accomplish). But you can't entirely blame the press in this case. They were egged on by the journals and university press offices that promoted the work,and, in some cases, the scientists themselves.

...

Unfortunately, things like well-established facts make for a lousy story. So instead, the press has often turned to myths, aided and abetted by the university press offices and scientists that should have been helping to make sure they produced an accurate story.


I'll go into the details of the ENCODE story near the end, but first we need a short history of "Junk DNA".

A history of "junk DNA"

The story begins with Susumu Ohno. In 1970, he wrote a book (Ohno, 1970a ) in which he laid out the argument for the role of gene duplication in evolution. We now know that it does indeed play its part. One thought experiment he had regarded genes that were duplicated (in his example, three sequences sharing the same sequence) and not under pressure by selection any more. If there is no selective pressure, they would mutate and two out of three would likely serve no function, due to high mutation rates.

Ohno 1970a, p.62 wrote:[It is likely that] in a relatively short time, two of the three duplicates would join the ranks of 'garbage DNA'.


This was the first time anything like this was proposed. Only two years later, in another paper (Ohno, 1972) would he coin the phrase "junk DNA". So what was "junk DNA" or "garbage DNA" to him? Well it's based on a very well-known observation:

Ohno 1972 wrote:If we take the simplistic assumption that the number of genes contained is proportional to the genome size, we would have to conclude that 3 million or so genes are contained in our genome. The falseness of such an assumption becomes clear when we realize that the genome of the lowly lungfish and salamanders can be 36 times greater than our own.


As we now know, we have roughly 20,000 genes, which fit well with Ohno's prediction of no more than 30,000 genes. It was also observed that there can be a lot of duplications and insertion of retroposons without affecting the body in any way. I talk about this later on, under the heading "pseudogenes".

At the time of Ohno's writing, "junk DNA" was "meant to describe the loss of protein-coding function by deactivated gene duplicates, which in turn were believed to constitute the bulk of eukaryotic genomes". (Gregory, 2007)

A very important part follows:
As different types of non-coding DNA were identified, the concept of gene duplication as their source, and therefore "junk DNA" as their descriptor, found new and broader application. However, it is now clear that most non-coding DNA is not produced by this mechanism, and is therefore not accurately described as "junk" in the original sense.


So in the original sense, we don't have a lot of "junk DNA" after all. The important thing to know here is that the term has been butchered by the media to mean all non-coding DNA, which strictly shouldn't be called "junk DNA" but rather "pseudogene", coined in 1977 (Jacq et al. 1977) to describe a functionless gene. Now note the miscommunication: There is a difference between "junk" (stuff one keeps) and "trash" (stuff one throws out). This was noted in 1988:

Brenner 1998 wrote:There is the rubbish we keep, which is junk, and the rubbish we throw away, which is garbage.


And in 1990, Brenner said the following:
Image
(S. Brenner, The human genome: the nature of the enterprise (in: Human Genetic Information: Science, Law and Ethics, No. 149: Science, Law and Ethics, Symposium Proceedings (CIBA Foundation Symposia) John Wiley and Sons Ltd 1990, Source) <-- One problem with that blog post is that much of it is wrong. I merely provide the source to show where I got the picture from.

And even in 1973, Ohno suggested a potential function for "junk DNA":

Ohno, 1973 wrote:The bulk of functionless DNA in the mammalian genome may serve as a damper to give a reasonably long cell generation time (12 hours or so instead of several minutes)


Gregory, 2007 wrote:From the very beginning, the concept of "junk DNA" has implied non-functionality with regards to protein-coding, but left open the question of sequence-independent impacts (perhaps even functions) at the cellular level. "Junk DNA" may now be taken to imply total non-function and is rightly considered problematic for that reason, but no such tacit assumption was present in the term when it was coined.


Gregory goes on to make a very astute observation: If there is no function for all genes, creationists are in serious trouble.

Gregory, 2007 wrote:[This is why] all non-coding DNA must, a priori, be functional.

To satisfy this expectation, creationist authors (borrowing, of course, from the work of molecular biologists, as they do no such research themselves) simply equivocate the various types of non-coding DNA, and mistakenly suggest that functions discovered for a few examples of some types of non-coding sequences indicate functions for all (see Max 2002 for a cogent rebuttal to these creationist confusions). Case in point: a few years ago, much ado was made of Beaton and Cavalier-Smith's (1999) titular proclamation, based on a survey of cryptomonad nuclear and nucleomorphic genomes, that "eukaryotic non-coding DNA is functional". The point was evidently lost that the function proposed by Beaton and Cavalier-Smith (1999) was based entirely on coevolutionary interactions between nucleus size and cell size.


Apart from the above mentioned potential function for "junk DNA", many more have been identified since:

Gregory, 2007 wrote:Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006) or retroviruses (e.g., Bremmerman 1987) or fluctuations in intracellular solute concentrations (Vinogradov 1998), serving as binding sites for regulatory molecules (Zuckerkandl 1981), facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001), inhibiting recombination (Zuckerkandl and Hennig 1995), influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997), increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982), maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995), coordingating genome function (Shapiro and von Sternberg 2005), and providing multiple copies of genes to be recruited when needed (Roels 1966).


In addition, I believe one can add both Epigenetics and Evo-Devo to that list.

Finally, Gregory notes the following:

Gregory, 2007 wrote:More broadly, those who would attribute a universal function for non-coding DNA must bear the following in mind: any proposed function for all non-coding DNA must explain why an onion or a grasshopper needs five times more of it than anyone reading this sentence.


Pseudogenes

Now I need to explain pseudogenes. I think the easiest way is to use this picture from the wikipedia article, which I modified for the purpose of illustration:
Image

As you may know, amino acids are encoded by reading DNA sequences in triplets. If, as in the above sequence, an insertion, deletion and point mutation occurs, the triplets are read differently. The results in amino acid encoding are shown above. If the new sequences produce premature stop-codons or, as in this case, simply different amino acids, genes may not be activated and proteins may not be produced. Sometimes they are encoded but do not actively help the organism.
These are then called pseudogenes.

The ENCODE delusion

A few months ago, the ENCODE staff published some research, which prompted the following statement by the EFF:
EFF wrote:On September 19, the Ninth Circuit is set to hear new arguments in Haskell v. Harris, a case challenging California's warrantless DNA collection program. Today EFF asked the court to consider ground-breaking new research that confirms for the first time that over 80% of our DNA that was once thought to have no function, actually plays a critical role in controlling how our cells, tissue and organs behave.


But as I showed above, functions for "junk DNA" have been known since before the term was even coined! This is what I'm talking about when criticizing the way scientists convey science and the way newspapers bring it to the public.

But let's back up a little. ENCODE has been working for quite some time now and, as you would expect, it has been talked about since at least 2007. (Arthur Hunt on Panda's Thumb, 2007) Even then, Creationists wanted to claim what they claim now, namely that all DNA has a definite function. There was (at least) one problem for them: A 2005 paper (Wyers et al. 2005) showed that "much of the RNA made by a cell is thrown away. This includes RNA encoded by intergenic regions." (Quote from Arthur Hunt, 2007)

PZ Myers documents a second story, with a 2010 paper (van Bakel et al. 2010) explaining once again that genes only make up about 2% of the genome, while the rest is non-coding.

That takes us back to the 2012 report from ENCODE. They claimed that 80% of the genome serves some biochemical function, with "function" being defined as participating "in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type". That's where the real problem in communication lies: The definition of the word "function".

PZ notes:
PZ Myers wrote:That isn't function. That isn't even close. And it's a million light years away from "a critical role in controlling how our cells, tissue and organs behave". All that says is that any one bit of DNA is going to have something bound to it at some point in some cell in the human body, or may even be transcribed. This isn't just a loose and liberal definition of "function", it's an utterly useless one.


I'll try to make this as clear as possible, so I'll draw on an analogy. Imagine you found two ball-point pens. One of them is a normal pen, the other lacks the ball-point. The first pen has a definite function: To write. The second one may have other functions (like removing ear-wax from your ear), but that's not a definition of function any sane person would recognize.
The same happened to ENCODE: The way they define "function" is so broad that it's absolutely useless. Indeed, much randomly generated DNA can be said to have "function" under this definition.

Also note that in his blog, Ewan Birney (kind of) explains what "function" means in ENCODE terms. What's noticeable is that it could just as well have been swapped for "specific biochemical activity", which takes the wind out of the sails completely.
In another Q&A point, he said that using the 80% number instead of the 20% functional bases (notice a difference?) was used to... hype up the story. That's basically it.

Ewan Birney Q&A wrote:Q. Ok, fair enough. But are you most comfortable with the 10% to 20% figure for the hard-core functional bases? Why emphasize the 80% figure in the abstract and press release?
A. (Sigh.) Indeed. Originally I pushed for using an "80% overall" figure and a "20% conservative floor" figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader, they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to "4 million switches", and that represents the bound motifs and footprints.

We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity.


And again from Arstechnica:

So even as the [2007] paper was released, we already knew the ENCODE definition of "functional impact" was, at best, broad to the point of being meaningless. At worst, it was actively misleading.

...

In the lead paper of a series of 30 released this week, the ENCODE team decided to redefine "functional." Instead of RNA, its new definition was more DNA focused, and included sequences that display "a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure)." In other words, if a protein sticks there or the DNA isn't packaged too tightly to be used, then it was functional.

That definition nicely encompasses the valuable regulatory DNA, which controls nearby genes through the proteins that stick to it. But,and this is critical,it also encompasses junk DNA. Viruses and transposons have regulatory DNA to ensure they're active; genes can pick up mutations in their coding sequence that leave their regulatory DNA intact. In short, junk DNA would be expected to include some regulatory DNA, and thus appear functional by ENCODE's definition.

...

The ENCODE team itself bears a particular responsibility here. The scientists themselves should have known what the most critical part of the story was,the definition of "functional" and all the nuance and caveats involved in that,and made sure the press officers understood it. Those press officers knew they would play a key role in shaping the resulting coverage, and should have made sure they got this right. The team has now failed to do this twice.


I've got another five blog-posts to go through, a summary of which I will add to this post, but for now I'll conclude:

1) "Junk" DNA was, from the moment of its conception, a misnomer. Just like "Big Bang" falsely conjures the image of an explosion, "junk DNA" falsely conjures the image of complete non-function or garbage. However, in both cases that's not consistent with what scientists have been saying even before the term was coined. "Junk DNA" should not be in common usage. A more precise term would be "pseudogene".

2) Conveying what "junk DNA", non-coding DNA and pseudogenes are, as well as the nuanced differences between the terms, is a difficult job. Sadly, neither scientists nor journalists have done a good job of explaining the terms. It would be interesting to make an extremely careful and detailed YT series on this subject.

3) Much of the ENCODE hype rests on the definition of the term "function". If the general public and creationists were aware of what "function" means in ENCODE terms, the hype would almost completely fade away. Note that I'm not saying that the results were wrong, inconclusive or not worthy of recognition, I'm simply saying that they were over-hyped. (Which would put them into the second circle of scientific hell!)

4) This problem also creates an opportunity. We now understand what we did wrong and this may encourage scientists to be more careful in the future when explaining things. I hope to make a blog series on the public understanding of science soon and this will be one of my focuses.



Below are all the references used in the creation of this post. The first one is only scientific papers, the second one is blog posts and opinion pieces.
Bob, if you want to you can reply now. Any additions I make won't really affect the overall picture any more.



"Sometimes people don't want to hear the truth because they don't want their illusions destroyed." ― Friedrich Nietzsche

"I shall achieve my objectives through the power... of Science!" --LessWrong
Last edited by Inferno on Sat Dec 08, 2012 12:10 pm, edited 1 time in total.
Fri Dec 07, 2012 11:59 pm
Dragan GlasContributorUser avatarPosts: 3210Joined: Mon Dec 14, 2009 1:55 amLocation: Ireland Gender: Male

Post Re: Aron Ra vs Bob Dutko

Greetings,

BobEnyart wrote:
Dragan Glas wrote:With all due respect Mr. Enyart, none of the above disproves either the accepted age of the Earth or, for that matter, the theory of evolution.

The idea that percentages of genes being "shared" by various life forms somehow disproves the theory of evolution is like saying that isomers disprove chemistry.

...It's not surprising that HGT is prevalent in the evolution of micro-organisms...

The modern "Tree of Life" is a banyan...

James

Hi James! Does it disprove the Jerry Coyne/AronRa claim that the nonconformist genetic sequence phenomenon is mostly in bacteria, except for an odd gene here and there?

No, it doesn't.

Is it possible that your confusion arises from mistaking HGT followed by vertical gene transfer (VGT) with VGT followed by HGT?

And I'm not sure what this has to do with what I posted.

BobEnyart wrote:Thanks for the description of an isomer. I use them as an analog for explaining to folks that a particular protein sequence could fold in countless different ways, whereas often, the particular shape of a protein is crucial for many functions vital for life. So that's another of hundreds of hurdles that abiogenesis would need to cross, before the first reproducing organism began functioning, and thus, before Darwinian natural selection could help find those functional forms.

There are two points you make here - one regarding the impossibility of abiogenesis and the evolution of proteins necessary for life.

Firstly, as I've posted elsewhere, biochemistry - the chemistry of life - is a subset of chemistry: given the right conditions, life can't help but occur.

Abiogenesis is a natural consequence of the laws of chemistry.

Secondly, evolution favours non-lethal mutations - those which are either helpful or, at least, neutral - in their effect on the survival of an organism.

Natural selection would filter out any mutations which are lethal to survival - it shouldn't be astonishing, therefore, to find that the proteins that are left are those that are necessary for life.

BobEnyart wrote:But to your question.

Question?

:? What question?

I didn't pose a question - I simply posted some observations concerning what you'd posted.

BobEnyart wrote:Evolution as a theory makes fundamental predictions, and predictions are the stuff of validating or refuting theory. For years we've been highlighting when (not minor but) MAJOR predictions of the Big Bang, an old Earth, and neo-Darwinism, fail in dramatic ways.

The fact is, they don't - Creationists thinking that they "fail in dramatic ways" only shows that they don't understand the science and the scientific method.

BobEnyart wrote:For example, I think you'd agree that while Darwinists say the chimp is our closest relative, theory has always put the Kangaroo quite a bit further from us on the tree of life (although of course closer than many other organisms, like a nautiloid -- remember the nautiloids). Because the kangaroo is somewhat distant from humans on Darwin's tree, Australian evolutionary geneticists were rather shocked by what they found inside joey. As we've reported on air, the director of Australia's Kangaroo Genomics Centre, Jenny Graves, reports that "There [are] great chunks of the human genome"¦ sitting right there in the kangaroo genome." And the 20,000 genes in the kangaroo (roughly the same number as in humans) are "largely the same" as in people, and Graves adds, "a lot of them are in the same order!" That's some HGT!

As I said earlier, you appear to be confusing HGT + VGT with VGT + HGT.

And, also, as I said earlier, "shared" percentages of genes doesn't disprove evolution - it's what you'd expect if it's true, but not for creationism

Jerry Coyne posted a couple of years ago regarding a paper by Douglas Theobald published in Nature, regarding a single origin for modern life.

If you can access the original article, read it - along with Coyne's, Myers', Matzke's and Than's: they're well worth reading.

BobEnyart wrote:And the sponge genome is even more wildly unlike what neo-Darwinism ever lead the evolution community to predict. So, we're not in the least pointing out that we're all learning something new in these studies. That's expected, and always great. It's that what we're learning is significantly contrary ("shocking", "horrendous", "jaw-dropping", etc.) to Darwinian expectations.

And still, none of this disproves evolution - it merely astonishes the scientists at how evolution actually works.

BobEnyart wrote:DINOS: I say to Aron, they've discovered dinosaur soft tissue. He says, no they haven't. I say yes, they have found blood vessels, blood cells, hemoglobin, etc., and other cells and proteins from a number of different dinosaurs. No they haven't; it's bacterial biofilm contamination. OK. So now, the LoR guys mostly deny what Aron was overly denying. Why? Because dinosaur soft tissue is not what evolutionists expect, but from studies on Egyptian mummies, with protein, acid racemization, and DNA half-life estimates, etc., Nature, Science, etc., are publishing papers finding what fits into the creationist model, but what is shocking to the evolutionists.

In saying "soft tissue", you're still making the same error as mistaking "fossil" for "bone".

BobEnyart wrote:JUNK: I say to famed PhD anti-creationist Eugenie Scott in 1997 on national TV regarding her "Junk DNA" claim against creation (which was shared by virtually the ENTIRE Darwin community) that as genetic science advances, we're likely to learn that those billions of nucleotides that they claimed affirmatively had no function actually had function that we were still to discover. She disagreed, and now Nature 2012 publishes results from 440 researchers that 80% of the human genome has function, with the project lead predicting that will go to about 100% (which is undeniably, at least, the general direction of the trend).

The term "junk", as used at the time, did not mean "without any purpose ever" - the thought, at the time, was that this was left-over from our evolutionary history; that it had played a vital part in the past but was not "actively required" in the present.

One might think of it like a scar - it doesn't do anything now but is a record of a event in your past.

Also, even if you gave the right answer for the wrong reason, does that make your beliefs right? ("God created man - therefore, everything in our DNA must have a purpose".)

BobEnyart wrote:NAUTILOIDS: I say to Aron that there are nautiloids buried in limestone at the base of the Grand Canyon, 15% buried vertically, and that even one would have a hard time being buried if the limestone were laid down slowly as old earthers claimed. He says, No. And I ask, what if they're there, and buried like that, would that provide evidence that the limestone was rapidly deposited? And he says, "No, not even if they existed." http://www.leagueofreason.co.uk/viewtopic.php?p=137751#p137751

What you don't ask is, if 15% were buried vertically - presumably due to "The Flood" - why weren't the other 85% buried vertically?

The explanation for their burial, which is the right one, is that which explains the larger percentage, not the smaller.

And if you're going to say "The Flood", then why were they buried alone instead of higgledy-piggledy with all the other fauna - and flora - from the same location, if not the world?

And that is assuming this 15% figure is correct - I've seen other Creationists claim 25%.

And how did they arrive at either figure exactly?

And Aron already addressed this.

Also, see Ocean Floor Sediments for an explanation of how sediments form.

BobEnyart wrote:James, ask yourself if that is a reasonable answer. Aron denied that there are millions of such nautiloid fossils in that layer (even though they're easily found, and found as far away as on the Strip in Las Vegas where that same layer extends to). Yet, while there could be a reasonable disagreement about how prevalent, and the number, of nautiloids there, I don't believe there are geologist currently working the canyon who would deny that they are there. So, don't you agree that nautiloids buried in limestone represent hard scientific data, and that data, whatever it is, should be acknowledged, and if there are a percent of those nautiloids buried vertically, that this would be significant evidence that would require a reassessment of how slowly or rapidly that limestone was deposited. After all, it's probably be tough for a two-foot nautiloid to stand on its head for tens of thousands of years while an imperceptibly slow limestone shower buries it over millennia. And for this, LoR mocks me and praises Aron.

Aron may have doubted and/or denied their existence on the show - which is understandable, as he had no means of verifying your claim(s) on-the-fly.

In the written debate, as I've mentioned above, he addressed your claim regarding these nautiloids, which turns out to be questionable.

BobEnyart wrote:So, with the never-ending stream of MAJOR evolutionary predictions failing (as we document on air, from the mouths of the evolutionists... who admittedly, yes, still remain evolutionists), we think this is strong negative evidence against the old-earth claims, and to that we add many other lines of evidence as at youngearth.com. And between Aron's middle finger, and the relentless mocking here on LoR that as a creationist I can't even read an article, it seems by their zero-concession policy, that the bombast is coming from the evolutionists.

Thanks for asking.

-Bob Enyart
http://KGOV.com/science

"Old Earth" claims are backed up by science - YEC isn't, and also fails on theological/philosophical grounds.

With all due respect, Mr. Enyart, you are sadly misguided in your belief in YEC and your grasp of science has been all but crippled by a overly religious upbringing.

Kindest regards,

James
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"The Word of God is the Creation we behold and it is in this Word, which no human invention can counterfeit or alter, that God speaketh universally to man."
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Sat Dec 08, 2012 12:24 am
BobEnyartUser avatarPosts: 45Joined: Sat Jan 28, 2012 2:19 amLocation: Denver, Colorado, USA Gender: Male

Post Re: Aron Ra vs Bob Dutko

nemesiss wrote:if this is a discussion on the age of planet earth, then the following points your points have no place om the discussion, for they create 'white noise';
- Genomes and Earth History
- Dinosaur soft tissue
- Dinosaur Layer Biological Material
- National Parks correcting old-earth-biased signs

if i take your statement serious, apart from evolution (which is an explenation for the diversity of life), Darwin also had another theory with regards to the age of the sun, stars and galaxies? i have to say i'm sorry, but that's just wrong.


Hi nemesiss, you should be able to agree with these statements (even if you are an ardent atheist or evolutionist)
1. If the Earth and Sun are only thousands of years old, then Darwin's theory of how life on Earth diversified must be false
2. Regardless of what other evidence supports or undermines an old earth, if Darwinism is false, it is therefore not evidence of an old Earth.

Another way of saying this is that Darwin's theory requires an old Sun and Earth (which is what I was trying to get across before; I guess I didn't do a great job of it), and if evolution is true, then the Earth must be millions or billions of years old.

In these ways these matters are related. Thus for example, if there is short-lived Carbon 14 in diamonds and dinosaur bones, and contamination and neutron capture can be ruled out, that alone falsifies Darwinism.

Thanks,

-Bob Enyart
http://kgov.com/how-to-date-a-dinosaur
Taking on all atheists over at rsr.org/atheists.
Sat Dec 08, 2012 1:12 am
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australopithecusLime TordUser avatarPosts: 4347Joined: Sun Feb 22, 2009 9:27 pmLocation: Kernow Gender: Time Lord

Post Re: Aron Ra vs Bob Dutko

A cursory google search couldn't find enough facepalm jpegs to adequately describe that post.
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Sat Dec 08, 2012 2:47 am
he_who_is_nobodyBloggerUser avatarPosts: 3498Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Aron Ra vs Bob Dutko

I have been catching up on this thread (I was out of town for a few days) and I must correct the falsehoods BobEnyart made in just this one post before reading any further. BobEnyart totally misrepresented everything AronRa said. I am sorry if someone else already covered this later on, but I just could not take any more falsehoods from BobEnyart. Furthermore, I do not understand why anyone would misrepresent another person's position in a written forum. It is so easy to go back and show just how wrong BobEnyart is with AronRa's own quotes.

BobEnyart wrote:I say to Aron, they've discovered dinosaur soft tissue. He says, no they haven't.


Wrong BobEnyart:

AronRa wrote:As I already told you, I had already read Schweitzer's paper. I also know one of the guys on her team, and we talked a lot about a couple years ago. He told me that Schweitzer and Horner both liked to stir up controversy, but that what she found was none the less significant, because it forced a vast improvement of our earlier understanding of fossilization. My impression was this, she showed that very large bones, properly buried under the right conditions could effectively insulate the core sufficiently that isolated microscopic sections could contain original material not fully fossilized, meaning that demineralization might restore some original properties. Chemical decomposition would of course occur even then, (much the pity) so that these wouldn't be exactly what they were anymore, but the implications were still exciting to me at the time. That's when I saw a documentary wherein Schweitzer and Horner confirmed their hypothesis on a second very large femur buried under similar conditions.

The first I had ever heard of this was the story you cited "providing molecular support for the hypothesis that modern birds are descended from dinosaurs".Soon afterward came the creationists' claims of them having found actual blood cells and so on. But it turned out this never happened. Somehow creationists had turned "seven fragmentary chains of amino acids, the building blocks of proteins" into full-blown DNA ready for cloning.

I will grant that -once demineralized- these may again be 'soft' compared to the surrounding matrix, and I will grant that the word 'tissue' would apply to these structures regardless what they were made of. But you said these were original biological material, implying that they had not been fossilized at all, that they retained their original chemical composition, and were perhaps even still edible, and none of that is correct in any of the instances you listed. There are traces of original chemicals, especially hardier elements like metals and so on.


This was also quoted to you when you first started posting in this thread. This time I underlined the important parts. Furthermore, you should have read and known this when you were participating in the debate.

BobEnyart wrote:I say yes, they have found blood vessels, blood cells, hemoglobin, etc., and other cells and proteins from a number of different dinosaurs. No they haven't; it's bacterial biofilm contamination.


You were wrong about those too, which AronRa also corrected you during the debate. Again, this was quoted for you on this thread already and again, perhaps the underlining will help it stick in this time:

AronRa wrote:Your most compelling argument, seriously, was when you said that the heme from Horner's T-rex was used to immunize lab rats, generating antibodies. However even that study identified the source as ancient heme and hemoglobin break-down products, compounds derived from blood, but that were not actually blood anymore. So all you proved after two weeks of effort was what I had already told you three weeks ago.


Furthermore, here is where AronRa corrected you on your misunderstanding of blood vessels and cells:

AronRa wrote:The articles you cited described "recovery of what appear to be cells, blood vessels and tissues", meaning that they had not been confirmed. Understand that calling "structures morphologically reminiscent of vertebrate red blood cells" does not mean they are red blood cells. That's what they say when they have not been confirmed. Tissues are reported as 'preserved', because that's what fossilization does, but it doesn't mean preserving the original chemical composition. In fact, your citations say that these were fossilized at least to the point of having to be demineralized. One of your citations even says the collagen may be 'preserved' only as breakdown compounds per oxidative deamination, meaning that it was both fossilized and decomposed.


As you can see, AronRa never claimed that biofilm is what accounted for the blood vessels and cells you claimed were discovered. Stop creating straw men.

BobEnyart wrote:OK. So now, the LoR guys mostly deny what Aron was overly denying.


Wrong again BobEnyart. You are the one that is denying what AronRa has said from the beginning. Furthermore, if you were using standard definitions of the terms "soft tissue", "biological material", etc"¦ and not using them interchangeably, nearly all of the confusion that happened in the peanut gallery would have disappeared.

BobEnyart wrote:Why? Because dinosaur soft tissue is not what evolutionists expect, but from studies on Egyptian mummies, with protein, acid racemization, and DNA half-life estimates, etc., Nature, Science, etc., are publishing papers finding what fits into the creationist model, but what is shocking to the evolutionists.


Change evolutionists to scientists and you would be correct. These findings have led scientists to reexamine fossilization. However, the fact that trace soft tissues have been discovered does nothing to support the claims of a young earth or that the fossils themselves are young. One needs to overturn the established dates of the fossiliferous layers in order to do either of those. This problem is something you keep avoiding.

BobEnyart wrote:I say to Aron that there are nautiloids buried in limestone at the base of the Grand Canyon, 15% buried vertically, and that even one would have a hard time being buried if the limestone were laid down slowly as old earthers claimed. He says, No. And I ask, what if they're there, and buried like that, would that provide evidence that the limestone was rapidly deposited? And he says, "No, not even if they existed."


This paragraph was a total misrepresentation of what actually was stated. I will simply quote what was said:

AronRa wrote:
Would millions of nautiloids the size of your arm standing on their heads fossilized in limestone in the canyon provide evidence of rapid stratification Aron?
No, not even if they existed. Limestone can't form rapidly, (certainly not in the situation you're talking about) and the conditions you describe are not consistent throughout the site you claim, even according to other Bible-believing Christians.

"The nautiloids of Nautiloid Canyon are claimed to be aligned, indicating that they died in a strong current and yet, this writer visited this deposit in July, 1995, and found no alignment of any nautaloids anywhere in the Canyon. The authors ignore the stratification of fossils which are clearly found in layers--not mixed up as a flood would suggest."--John N. Clayton, author of 'Does God Exist'

Coincidentally Eugenie Scott gave a speech on the Grand Canyon at the G.A.C. in Melbourne, as she often does. In it she gave many instances of geology that young earth creationists simply can't account for. That talk hasn't been released on video yet. She has done several others, but I won't provide the links since you wouldn't watch them anyway. For the moment, I'll just quote her:

"I have examined these nautiloids in only a few localities within the Grand Canyon National Park, to which he [Steve Austin] was kind enough to direct me, where I noted that a nautiloid fossil occurred about once every 4 or 5 square meters. From this I infer that either Austin has collected most of the samples from these localities or the abundance of nautiloids claimed is exaggerated. However, unlike Austin, I hesitate to extrapolate from observations at a few isolated localities to a huge area. Furthermore, most of the nautiloid fossils I saw, and that Austin illustrates, were intact. Could they have survived the turbulence that must occur in a fast moving, subaqueous, debris flow? In nature, mass-kill events certainly occur , by red tides, volcanic eruptions, and storm-induced processes flows, for example. However, in order to recognize a mass-kill, we need to understand the population structure of the animals concerned, and to consider factors such as episodic spawning, variable growth rates, the complex diurnal behavior of cephalopods, and so on.
Evidence bearing on the question "Did this nautiloid assemblage accumulate instantaneously or over many generations?" should be present in the deposit itself. Do the dolomitization and the prominent chert horizon overlying the nautiloid bed represent diagenesis during a hiatus in deposition? Similarly, are Austin's "water escape tubes" actually poorly preserved animal burrows (Skolithos)? High concentrations of fossil nautiloids occur elsewhere, for example, in Morocco and in the Czech Republic. Ferretti and Krà­z (1995) describe several such examples in the Silurian of the Prague Basin and attribute them to the effects of surface currents or re-deposition in shallower environments by storm events during broad scale fluctuations in sea level. Why not the same in the Grand Canyon?"


Furthermore, you still have not answered how limestone formed rapidly in an aquatic environment. The nautiloids buried in limestone that you keep harping on about do more to show and old earth than they ever could do to show a young earth. Until you are able to explain how limestone can form rapidly in an aquatic environment, the point you keep trying to make with them is moot.

BobEnyart wrote:Aron denied that there are millions of such nautiloid fossils in that layer (even though they're easily found, and found as far away as on the Strip in Las Vegas where that same layer extends to).


As anyone can plainly see from what I quoted above, AronRa did not deny the existence of a layer of nautiloids; he denied that there were millions of them standing on their heads. He also provided citations that support that there were not millions found on their heads. Again, stop creating straw men.

This reminds me of how bad you misrepresented the mammoth wager.

This is just for the record:

BobEnyart wrote:Junk DNA


Gary Hurd wrote:Soon after the discovery of how DNA stored sequences used to replicate proteins there began a bidding war for research funds to specify the DNA sequences and identify their function. In the battle, non-coding sections were called "junk DNA" since there was no obvious function that could be intuitively connected with a particular gene. A protein coding sequence clearly had a function, even if what the protein did was unknown at the time. Since building a sequence data base was then extremely expensive (and boring), the argument against deciphering non-transcribed "Junk" won out. But, the possible functionality of "junk DNA" was raised in the late 1970s. The argument was simple: there was an evolutionary cost to making copies of useless DNA. Since this cost was being paid, the "Junk" must have a function. The human genome project was conceived after the discovery of polymerase chain reaction (PCR) in 1983. Many researchers were still objecting to spending scarce research money on non-coding sequences as late as 1989.

Some likely functions of this "junk" were discovered by geneticists in the late 1980s, reaching journal publications by the early 1990s. The development of automated sequencing machines around 2000 finally eliminated the last objections to sequencing "junk."

(See;
AD Riggs (1990) "Marsupials and Mechanisms of X-Chromosome Inactivation".
Australian Journal of Zoology 37(3) 419, 441 (Suggested that "junk DNA" would not be preserved without some function, identified control functions specifically as promoters of spreading).

J Brosius and S J Gould (1992) "On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA"" PNAS November 15, vol. 89 no. 22 10706-10710 (They propose that "junk DNA" is evolutionarily significant by providing raw material for future functions, is implicitly the source for current gene functions, and preserves the evolutionary history of organisms. Received 1991).

Emile Zuckerkandl, 1992, "Revisiting junk DNA" Journal of Molecular Evolution Volume 34, Number 3 / March, 1992 (Received 1991) (Suggested that "junk DNA" would not be preserved without some function, speculated that there were control functions).

What did the creationists have? ... The best they can do is a 1998 article by William Dembski. In an article for the Christian magazine "First Things," he noted the discovery of functionality by scientists (not by creationists) in portions of the human genome that had been considered as uninteresting "junk DNA" by many. Specifically, Dembski quotes Bodnar et al's 1997 abstract from, "Deciphering the Language of the Genome." To a competent reader, Dembski is defending creationism's position from scientific advances by attempting to co-opt them.

Bodnar, JW, J Killian, M Nagle, S Ramchandani (1997) "Deciphering the Language of the Genome." Journal of Theoretical Biology Vol 189, Issue 2, 21 November 1997 Pages 183-193).

Dembski, William A. (1998) "Science and Design" First Things 86 (October 1998): 21-27.

The ENCODE project began releasing reports with 30 articles published in the first week of September this year. They generated a great deal of excitement, and controversy. The first highly controversial topic was how they chose to define "functional" for DNA sequences. Basically, any segment of DNA that was transcribed by RNA was anointed as "functional." The directors of the project are already walking back from that claim. They weakly explained that the "public" might have been confused. Days later, a key project leader, Ewan Birney, Ph.D., was trying to justify using "80% functionality" in his press releases. His answer was to redefine "functional." In practical terms, "functional" became anything they could find that could bind somewhere. For what Birney admitted most people think of as "functional," the percentage falls hard to ~20%.

Here is a portion of his self commentary;.

Q. Ok, fair enough. But are you most comfortable with the 10% to 20% figure for the hard-core functional bases? Why emphasize the 80% figure in the abstract and press release?
A. (Sigh.) Indeed. Originally I pushed for using an "80% overall" figure and a "20% conservative floor" figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader, they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to "4 million switches", and that represents the bound motifs and footprints.

We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity.

http://genomeinformatician.blogspot.com ... ughts.html

Finally, the only thing holding back "the progress of genomic research" has been lack of money, and the religious-right blocking stem cell research.


Taken from a facebook comment, link is to his blog.
_BONES AND FOSSILS = LOVE_
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Sat Dec 08, 2012 9:35 am
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he_who_is_nobodyBloggerUser avatarPosts: 3498Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Aron Ra vs Bob Dutko

BobEnyart wrote:Hi nemesiss, you should be able to agree with these statements (even if you are an ardent atheist or evolutionist)
1. If the Earth and Sun are only thousands of years old, then Darwin's theory of how life on Earth diversified must be false


If by Darwin's theory you mean universal common descent, you are correct. Having a 6,000 - 10,000 year old earth does pose a problem for some aspects of evolutionary theory. However, that would in no way contradict natural or sexual selection, which where the theories Darwin actually proposed. That time span also would not disprove evolution, seeing as how evolution is an observed fact.

This reminds me, the first thing I usually ask a creationist when engaging them is to define evolution in its biological context. When I posed this to YesYouNeedJesus, he refused to answer (which was telling). BobEnyart, perhaps with your years of creationist research below your belt, you would be able to give the correct definition of evolution.

BobEnyart wrote:2. Regardless of what other evidence supports or undermines an old earth, if Darwinism is false, it is therefore not evidence of an old Earth.


BobEnyart, you do understand that if any argument is shown to be false it cannot be used as evidence of anything, right? This probably would seem to most to be a rhetorical question, but you have demonstrated that you will use debunked arguments long after they were refuted. Thus, I am truly curious if you understand that once something is proven wrong, it no longer can be used as an argument.

Furthermore, if by Darwinism you mean evolutionary theory, no one has argued that it proves an old earth. Stop creating straw men. Evolution would remain an observed fact whether the earth was young or old.

he_who_is_nobody wrote:In addition, it would be nice if you would address this post next time you returned.
_BONES AND FOSSILS = LOVE_
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Sat Dec 08, 2012 6:17 pm
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nemesissUser avatarPosts: 1259Joined: Sun Sep 13, 2009 7:29 pm

Post Re: Aron Ra vs Bob Dutko

BobEnyart wrote:
nemesiss wrote:if this is a discussion on the age of planet earth, then the following points your points have no place om the discussion, for they create 'white noise';
- Genomes and Earth History
- Dinosaur soft tissue
- Dinosaur Layer Biological Material
- National Parks correcting old-earth-biased signs

if i take your statement serious, apart from evolution (which is an explenation for the diversity of life), Darwin also had another theory with regards to the age of the sun, stars and galaxies? i have to say i'm sorry, but that's just wrong.


Hi nemesiss, you should be able to agree with these statements (even if you are an ardent atheist or evolutionist)
1. If the Earth and Sun are only thousands of years old, then Darwin's theory of how life on Earth diversified must be false
2. Regardless of what other evidence supports or undermines an old earth, if Darwinism is false, it is therefore not evidence of an old Earth.


Dear mr Enyart,
unfortunately i would have to disagree with you on this.
you statement would only have validity, if BOTH the calculation of age of the earth AND the theory of evolution were both dependent on a single piece of evidence. Based on the conversations held sofar, i'd say you think this piece of evidence would be fossils.
the biggest flaw to start with, is you assumption that there is a field of science, that is only maintained on a single piece of evidence. science uses multiple lines of evidence to assert that the answers obtained are as accurate as possible (though via new techniques the answer may be even more refined) and to prevent any such form of bias.

the next big flaw is your overestimation of a single piece of evidence that could turn over two major discoveries that have been thoroughly tested by thousands of people and perfected to be the most accurate it can possibly be.
If you would compair the first attempt at determining the age of the earth to our modern day understanding, it could be described as "the act of someone who has no f*cking clue what he/she was doing". technically this could be said from any field in science.


BobEnyart wrote:Another way of saying this is that Darwin's theory requires an old Sun and Earth (which is what I was trying to get across before; I guess I didn't do a great job of it), and if evolution is true, then the Earth must be millions or billions of years old.

In these ways these matters are related. Thus for example, if there is short-lived Carbon 14 in diamonds and dinosaur bones, and contamination and neutron capture can be ruled out, that alone falsifies Darwinism.

Thanks,

-Bob Enyart
http://kgov.com/how-to-date-a-dinosaur


another way of saying my previous statement, darwin's theory only requires life that can reproduce and diversify.
it does not matter for this principle if the earth is 4.6 billion years, 20 million years, 6000 years or that it was created yesterday. it would not even matter if the earth was formed even before the sun.

regarding your point of carbon-14, it would be indeed an interesting anomoly for the theory of evolution and an interesting case for physicists. a possibility that could be considered an explenation is that the object in question gotten encased in material that blocks radiation, hence why it could not release it radio-activity.
though that has be determined for each indiviual case if this is indeed the case or not perhaps another reason.

not sure how this works for darwinism, im not familiar with that.

if you wish to continue this point you try to make, i would suggest you work out how you would determine the age of the sun and/or the earth in detail in such a way that others can repeat your experiment. that you do not agree with the premise of an old-earth i do not mind, but if you wish to continue saying the earth can only be young, you'd need to be able to back it up with facts. if this suggestion is to difficult to yourself, i do not mind if you let someone else to it for you. i (and probably others too) would like to see the results, how they were obtained and be able to repeat the test ourselves.

is assume that with darwinism, you mean the theory of evolution.
Sat Dec 08, 2012 7:23 pm
BobEnyartUser avatarPosts: 45Joined: Sat Jan 28, 2012 2:19 amLocation: Denver, Colorado, USA Gender: Male

Post Re: Aron Ra vs Bob Dutko

he_who_is_nobody wrote:I have been catching up on this thread (I was out of town for a few days) and I must correct the falsehoods BobEnyart made in just this one post before reading any further. BobEnyart totally misrepresented everything AronRa said.

Hi hwin, it's fine if you want to quote Aron's interpretation of what he said on the air. But the purpose of our written debate, as he urged it and explained it, was to find out who's on-air assertions were false, and who's were true.

Here's the transcription of what was said on air which started 27 minutes into our third program (from this 1.5 minute audio link):
http://kgov.com/files/audio/bel/2011/Ar ... tissue.mp3

Bob Enyart: The soft tissue that we find, the Tyrannosaurus Rex that we've got original biological material [from, and] then they found it in a Mosasaur that's [allegedly] 80 million years old. Then they found it in...

AronRa: You don't have original biological material.

Bob Enyart: Yes you do.

AronRa: No you don't. I've read Schweitzer's paper [Mary S., Jack Horner, etc., Proc. Bio. Sci. 2007, and earlier in 2005]. I suggest you review it.

Bob Enyart: Well you need to read the last five years worth of refereed scientific journals including from everywhere... in Nature, Science, PLoS -- Public Library of Science, [PNAS, etc.]

AronRa: [dismissive laughter]

Bob Enyart: Ten universities [and institutes] just published a report, in the U.S. and [Europe], leading universities, I can list them for you, saying we have absolutely ruled out contamination. This is not biofilm. This is original...

AronRa: Are you going to argue that you have blood cells? ... I'm not even going to argue this for the moment. I've covered this in my series.

Bob Enyart: [Your YouTube video] is out-of-date. Because there are now dozens of institutions [acknowledging the tissue finds]. They're finding biological tissue, dinosaur tissue.

hwin, if you notice, Aron didn't say what you quoted above. What you quoted was Aron's spin of what he said. So, would you, or any of the regulars here on LoR, agree now that ONLY REGARDING THE EXISTENCE OF SOFT TISSUE, that what I said on the air was true, and Aron was wrong?

Thanks,

-Bob Enyart
Taking on all atheists over at rsr.org/atheists.
Last edited by BobEnyart on Sun Dec 09, 2012 4:13 pm, edited 1 time in total.
Sun Dec 09, 2012 4:04 pm
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australopithecusLime TordUser avatarPosts: 4347Joined: Sun Feb 22, 2009 9:27 pmLocation: Kernow Gender: Time Lord

Post Re: Aron Ra vs Bob Dutko

BobEnyart wrote:So, would you agree now, or any of the regulars here on LoR, that ONLY REGARDING THE EXISTENCE OF SOFT TISSUE, that what I said on the air was true, and Aron was wrong?


Based on what? The papers you've provided on this forum contradict your position, and in the above post in which you're asking us to decide whether you or Aron was correct you've provided no evidence, just a chat transcript.
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Sun Dec 09, 2012 4:09 pm
BobEnyartUser avatarPosts: 45Joined: Sat Jan 28, 2012 2:19 amLocation: Denver, Colorado, USA Gender: Male

Post Re: Aron Ra vs Bob Dutko

nemesiss wrote:
BobEnyart wrote:Hi nemesiss, you should be able to agree with these statements (even if you are an ardent atheist or evolutionist)
1. If the Earth and Sun are only thousands of years old, then Darwin's theory of how life on Earth diversified must be false
2. Regardless of what other evidence supports or undermines an old earth, if Darwinism is false, it is therefore not evidence of an old Earth.

Dear mr Enyart,
unfortunately i would have to disagree with you on this.

nemesiss, thanks for chatting. I'll leave this where it is for now. Hope you're okay with that.

-Bob Enyart
http://kgov.com/caterpillar
Taking on all atheists over at rsr.org/atheists.
Sun Dec 09, 2012 4:10 pm
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australopithecusLime TordUser avatarPosts: 4347Joined: Sun Feb 22, 2009 9:27 pmLocation: Kernow Gender: Time Lord

Post Re: Aron Ra vs Bob Dutko

BobEnyart wrote:nemesiss, thanks for chatting. I'll leave this where it is for now. Hope you're okay with that.


Why is it that whenever you can't refute someones argument you decide then is the best time to stop the debate? What's the next stop on this sad bus ride? Are you going to ignore nemesiss too?

At what point does your dishonesty end? It'll come to a point where you're ignoring everyone on the forum. If you have no intention of honest debate on this forum then you can leave whenever you like.
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Sun Dec 09, 2012 4:15 pm
InfernoContributorUser avatarPosts: 2298Joined: Thu Apr 30, 2009 7:36 pmLocation: Vienna, Austria Gender: Cake

Post Re: Aron Ra vs Bob Dutko

Bob, I posted a refutation of your Junk DNA claim above. See here. What say you?
"Sometimes people don't want to hear the truth because they don't want their illusions destroyed." ― Friedrich Nietzsche

"I shall achieve my objectives through the power... of Science!" --LessWrong
Sun Dec 09, 2012 5:27 pm
he_who_is_nobodyBloggerUser avatarPosts: 3498Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Aron Ra vs Bob Dutko

BobEnyart wrote:
he_who_is_nobody wrote:I have been catching up on this thread (I was out of town for a few days) and I must correct the falsehoods BobEnyart made in just this one post before reading any further. BobEnyart totally misrepresented everything AronRa said.

Hi hwin, it's fine if you want to quote Aron's interpretation of what he said on the air. But the purpose of our written debate, as he urged it and explained it, was to find out who's on-air assertions were false, and who's were true.


Oh so you were talking about the on air discussion and not the written debate. I see. Well, it appears AronRa was making a clarification (even a correction). I say this because in a live discussion, one is not always able to make clear what they are actually trying to say, but in a written forum, one has time to clarify their points. Either way, whether this is clarification or a correction, AronRa stated we had discovered soft tissue on February of 2012, yet as of just a few days ago, you are still arguing this issue as if AronRa did not admit that. Tell me BobEnyart, who is the one spinning this issue?

BobEnyart wrote:Here's the transcription of what was said on air which started 27 minutes into our third program (from this 1.5 minute audio link):
http://kgov.com/files/audio/bel/2011/Ar ... tissue.mp3

Bob Enyart: The soft tissue that we find, the Tyrannosaurus Rex that we've got original biological material [from, and] then they found it in a Mosasaur that's [allegedly] 80 million years old. Then they found it in...

AronRa: You don't have original biological material.

Bob Enyart: Yes you do.

AronRa: No you don't. I've read Schweitzer's paper [Mary S., Jack Horner, etc., Proc. Bio. Sci. 2007, and earlier in 2005]. I suggest you review it.

Bob Enyart: Well you need to read the last five years worth of refereed scientific journals including from everywhere... in Nature, Science, PLoS -- Public Library of Science, [PNAS, etc.]

AronRa: [dismissive laughter]

Bob Enyart: Ten universities [and institutes] just published a report, in the U.S. and [Europe], leading universities, I can list them for you, saying we have absolutely ruled out contamination. This is not biofilm. This is original...

AronRa: Are you going to argue that you have blood cells? ... I'm not even going to argue this for the moment. I've covered this in my series.

Bob Enyart: [Your YouTube video] is out-of-date. Because there are now dozens of institutions [acknowledging the tissue finds]. They're finding biological tissue, dinosaur tissue.


Compared with:

BobEnyart wrote:DINOS: I say to Aron, they've discovered dinosaur soft tissue. He says, no they haven't. I say yes, they have found blood vessels, blood cells, hemoglobin, etc., and other cells and proteins from a number of different dinosaurs. No they haven't; it's bacterial biofilm contamination. OK. So now, the LoR guys mostly deny what Aron was overly denying. Why? Because dinosaur soft tissue is not what evolutionists expect, but from studies on Egyptian mummies, with protein, acid racemization, and DNA half-life estimates, etc., Nature, Science, etc., are publishing papers finding what fits into the creationist model, but what is shocking to the evolutionists.


BobEnyart, you are now claiming that the section I quoted from this post (reproduced above for comparison) was based on the on air discussion, yet nowhere in what you transcribed was a discussion of blood vessels or hemoglobin. There was mention of blood cells, which AronRa brought up, and you brought up the only mention of biofilm.

You see BobEnyart, how I was confused, because in the written debate, you mentioned all those things and, as I pointed out, AronRa refuted all those points. Do you also see how none of what you paraphrased in the above quote is equivalent to the on air discussion? However, your responses are a fairly good representation of the written debate, but AronRa's responses bare no resemblance of what he actually said. BobEnyart, this is what we call spin. It appears, you spun that whole section out of your mind, and it reflects little of what happened in reality.

BobEnyart wrote:hwin, if you notice, Aron didn't say what you quoted above. What you quoted was Aron's spin of what he said. So, would you, or any of the regulars here on LoR, agree now that ONLY REGARDING THE EXISTENCE OF SOFT TISSUE, that what I said on the air was true, and Aron was wrong?


Again, BobEnyart, I was quoting what AronRa said in the written debate, thus he actually did say that. I was confused and thought you were referring to that, so I am sorry (even though your paraphrasing better fits the written debate than on air discussion). However, as I have pointed out, the only spin going on here is from you.

In your on air discussion, you were correct. It is a good thing AronRa corrected that back in February. BobEnyart, why do you keep bringing this up as if this was AronRa's position when it obviously is not? What is the point in misrepresenting AronRa's stance on this topic?

Furthermore, will you address the misrepresentation of AronRa when it came to your nautiloid claim or address the spin you created when it comes to junk DNA? Both of those were covered in my post as well, yet you only seemed to try to spin this bit in your favor, which did not really work for you either.
_BONES AND FOSSILS = LOVE_
(_'--------------------'_)
(_.--------------------._)
Sun Dec 09, 2012 7:37 pm
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he_who_is_nobodyBloggerUser avatarPosts: 3498Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Aron Ra vs Bob Dutko

This just occurred to me; I would just like to point out BobEnyart's slippery use of terms once again.

BobEnyart stated this:

BobEnyart wrote: I say to Aron, they've discovered dinosaur soft tissue.


However, BobEnyart is claiming that he was referring to the on air discussion where he said this:

BobEnyart wrote:The soft tissue that we find, the Tyrannosaurus Rex that we've got original biological material [from, and] then they found it in a Mosasaur that's [allegedly] 80 million years old. Then they found it in...


BobEnyart, as I have pointed out before, original biological material does not always equal soft tissue. One can discover original biological material (such as heme) which would not be the same as soft tissue (such as blood cells).

Thus, I must go back and correct what I said here:

he_who_is_nobody wrote:In your on air discussion, you were correct. It is a good thing AronRa corrected that back in February. BobEnyart, why do you keep bringing this up as if this was AronRa's position when it obviously is not? What is the point in misrepresenting AronRa's stance on this topic?


AronRa was correct to state that Schweitzer et al. did not discover original biological material, they found break down products, which could be considered soft tissue after demineralization (e.g. collagen).

BobEnyart, please stop mincing your terms. It confuses the whole discussion and leads to useless arguments. I brought this up in the peanut gallery, but I really wish you would state exactly what you mean when you state "soft tissue", "original biological material" and all the other terms used for this discussion. Once this is done, perhaps you will stop mincing the terms in your posts and we can actually focus on the real discussion instead of constantly arguing semantics.
_BONES AND FOSSILS = LOVE_
(_'--------------------'_)
(_.--------------------._)
Sun Dec 09, 2012 8:47 pm
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IsotelusBloggerUser avatarPosts: 317Joined: Tue Nov 02, 2010 12:59 am Gender: Tree

Post Re: Aron Ra vs Bob Dutko

I'll post this again, as it might have been missed (understandably).

Isotelus wrote:
BobEnyart wrote:Hi Isoltelus, hey, if you carved teeth out of stone, and surgically inserted them into a cow's mouth, do you think that Prof. Erickson would predicted that "they would function perfectly"?

-Bob Enyart
Real Science Friday


The question is nonsensical, and it missed my point entirely, but I'll bite (pun intended). The answer is yes, I would certainly hope he would predict so. Are the function of dentures or implants impeded by their lack of biological and organic material? But in all seriousness, I am disappointed that you do not see the futility in relying on quotes from news articles rather than what they wrote in their actual research article. Testing of the teeth found microscopic bone tissue (also mineralized), however collagen was absent, as was the pulp that would have filled the gaint tubercles. It also states that the fossil specimens chosen for the study were from two formations that often yield samples with fine microstructures preserved. This is the case with the Edmontosaurus teeth studied here, and is precisely what I was alluding to when I said Erickson was referring to the structural detail in the teeth.


I hope no one minds me going a bit farther back in the discussion, but I thought I would address this one as well, since it was not included in the debate with Aron. You have brought it up twice, but it has not yet been discussed here:

BobEnyart wrote:And I'll add to that NS article this one example (out of the constant examples reported in the literature). If Coyne and Aron and LoR were correct, and I as the opposing creationist were wrong, then Darwin's tree of life would still be drawn showing a cow and a horse somewhat closely related, with bats flittering about elsewhere on the tree. But a paper in PNAS, based on DNA sequencing, says that horses, unexpectedly, are closer to bats than to cows. Holy cow. That's not an example of genetics doubly confirming Darwin's tree, as Aron claims, but of what New Scientist claimed, as a courageous and honest assessment of the data.


First I'll explain what the PNAS paper said, then I'll explain why keeping up to date with the scientific literature is important. Horses and cows are perhaps not as closely related as you might think; they are, after all, separated into two different orders that split around the early Eocene (perissodactyla and artiodactyla, respectively). That being said, they are grouped in the same superorder, Laurasiatheria, which also includes Ferae (dogs, cats, pangolins), Eulipotyphla (hedgehogs, moles, etc), and most recently, Chiroptera (bats). Sure, that was surprising, but it still didn't harm the "tree of life". Now, when NS reported on the paper in question, they made a mistake by stating that the proposed unranked group within Laurasiatheria that Perissodactyla, Ferae, and Chiroptera were included in, called Pegasoferae, included cows and whales (Cetartiodactyla). This might have given the illusion that the actual PNAS paper showed Cetartiodactyla more closely related to Perissodactyls than they actually are. In fact, Cetartiodactyla was the sister group to Pegasoferae. There is really no excuse for NS to make this mistake, as the members of Pegasoferae are clearly stated within the paper, which is public access. Duh. Furthermore, earlier papers had already suggested that Chiroptera belonged in Laurasiatheria (Liu et al., 2001, as an example). This same paper also found evidence that Chiroptera are most closely related to another basal group within Laurasiatheria, but outside of Pegasoferae: Eulipotyphla. Now I'll highlight the importance of staying up to date with the scientific literature. There have been a number of much more recent papers that have shown Pegasoferae is not actually natural group, i.e., will no longer be used, but nevertheless show Chiroptera as a more basal group within Laurasiatheria; diverging after Eulipotyphla, but prior to Ferae, Perissodactyla, and Cetartiodactyla.
This is what the most current research shows:

Edit 2: Inferno was kind enough (everybody thank him!) to draw up this simplified version of the cladograms provided by the paper linked above. Take note particularly of the positions of Chiroptera, Perissodactyla, and Cetartiodactyla:
Image

If you know how to read a cladogram, you will see that this one does not indicates bats are more closely related to horses than cows.
Punnet square summer camp: Be there or be square!
Last edited by Isotelus on Tue Dec 11, 2012 9:49 pm, edited 2 times in total.
Sun Dec 09, 2012 9:44 pm
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