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Author Topic:   Looking for the Super-Genome. -And it ain't found
ChibiQ
Junior Member (Idle past 4046 days)
Posts: 3
Joined: 11-26-2007


Message 46 of 66 (436770)
11-27-2007 1:43 PM
Reply to: Message 45 by jar
11-27-2007 1:26 PM


Re: No evidence from you yet, jar. Please provide
"Some of the DNA from the tsar's mitochondria--cellular organelles with their own DNA--didn't quitematch that of his living relatives. Forensic experts thought that most people carry only one type ofmitochondrial DNA(mtDNA), but the tsar had two: The same site sometimes contained a cytosineand sometimes a thymine. His relatives had only thymine, a mismatch that fueled controversy overthe authenticity of the skeletons.

"The question of the tsar's bones was finally put to rest after the remains of his brother, the Grand Duke of Russia Georgij Romanov, were exhumed; the results of the DNA analysis were published in Nature Genetics in 1996. Like the tsar, the duke had inherited two different sequences of mtDNA from their mother, a condition known as heteroplasmy."

The duke and the tsar lived less than 150 years apart. 2, maybe 3 generations sounds reasonable, and even if it were a couple more, would that matter?


This message is a reply to:
 Message 45 by jar, posted 11-27-2007 1:26 PM jar has responded

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Wounded King
Member (Idle past 2174 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 47 of 66 (436774)
11-27-2007 1:56 PM
Reply to: Message 46 by ChibiQ
11-27-2007 1:43 PM


Re: No evidence from you yet, jar. Please provide
What is this example supposed to demonstrate?

The Duke and the Tsar had the same mitochondrial DNA down to having the same extra form inherited from their mother. Is your suggestion that Eve had multiple mtDNA types present in her germ cells so that her offspring were highly heterogeneous? Are you suggesting this persisted? If so then that is exactly the sort of super-genetic claim that Jar is looking for evidence of.

The example of cases of heteroplasmic mitochondrial inheritance certainly aren't a sufficient demonstration.

If this is supposed to be evidence of any sort of an accelerated mutation rate in mtDNA I am baffled since it has nothing to do with mutation rates since the mutation is supposed to have been preexisting in the mother.

So what has your example got to do with mtDNA mutation rates? In addition the occurrence of a single point mutation is not sufficient to establish a mutation rate.

TTFN,

WK


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jar
Member
Posts: 30934
From: Texas!!
Joined: 04-20-2004


Message 48 of 66 (436778)
11-27-2007 2:15 PM
Reply to: Message 46 by ChibiQ
11-27-2007 1:43 PM


Re: No evidence from you yet, jar. Please provide
HUH?

What does any of this have to do with the topic?


Aslan is not a Tame Lion
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Hyroglyphx
Member
Posts: 5622
From: Austin, TX
Joined: 05-03-2006


Message 49 of 66 (436912)
11-28-2007 12:22 AM
Reply to: Message 1 by jar
09-24-2006 2:39 PM


Re: written in the Year 5767
So, if there was some super-genome, why are there no signs of it in the people, animals, plants, spores and pollen contemporary with Adam?

Who says there was a super-genome? Who made that claim?


“This life’s dim windows of the soul, distorts the heavens from pole to pole, and goads you to believe a lie, when you see with and not through the eye.” -William Blake
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Wounded King
Member (Idle past 2174 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 50 of 66 (436933)
11-28-2007 6:37 AM
Reply to: Message 49 by Hyroglyphx
11-28-2007 12:22 AM


Origin of the 'super genome'
The idea was principally Faith's although I'm not sure if she coined the term and I doubt the idea was original with her. Randman occasionally put forward similar ideas and John Davison's prescribed evolutionary hypothesis basically relies on the existence of a super genome as well.

It isn't necessarily a very specific term as it can encompass a number of concepts. The simplest form would be consistent with the idea of what we think of as evolution, or microevolution within kinds for the creationists, as the ongoing degradation of several original created genomes. This original genome would need to be much larger than a modern genome as it would have many redundant sequences which serve to provide much of the genetic diversity we see today in modern species.

So the simplest form would be a super genome which had sufficient genetic material to produce all the geneti diversity we see today.

Davison's formulation was perhaps even stranger. As you may recall he believed in the process of evolution in terms of the descent from possibly several distinct common ancestors for different high order clades, nt low enough to be considered kinds though, but denied that the evolutionary process was still continuing or that it operated in line with the thinking of current evolutionary science. Instead he proposed that evolution was driven by changes in chromosomal organisation occuring during a process he called semi meiosis. The restructuring ocurring during semi meiosis changed the genome so as to allow the expression of previously latent genetic elements and leading to the saltationary emergence of a new species or significant new trait.

Randman's formulation was hard to pin down but seemed to be more concerned with the effect of quantum and internal features relating to DNA driving genetic changes along specific routes, rather than actually requiring a larger genome.

The main feature of all these types of 'super genome' is that they use front loading, of whatever form, to explain the current genetic diversity we see, whether it is from changes within created kinds or from evolution of everything from a common ancestor.

Faith and John Davison's ideas call for a number of genetic factors and effects which are entirely theroretical and which have no evidence to support them as far as I know. It is hard to think of a way to test Randman's formulation since in many ways it is simply a quantum mechanical version of 'god did it' where we cannot discriminate between the stochastic occurrences of mutation from natural causes and specific mutations directed by some mysterious force. Presumably these are the sort of signals which a science of ~ID ought to be able to detect.

Does this clear the idea up a little?

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
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jar
Member
Posts: 30934
From: Texas!!
Joined: 04-20-2004


Message 51 of 66 (436964)
11-28-2007 10:12 AM
Reply to: Message 49 by Hyroglyphx
11-28-2007 12:22 AM


Re: written in the Year 5767
WK covered most of it, but there is a little more. The first time I remember hearing the idea put forward was in relation to the then new information being found that there were different genetic groups. The idea presented was that Adam and Eve's genes would have contained all the possible variations and that their children just inherited some of the genetic information from the parents. This was, IIRC the beginnings of the Super Genome idea.

The concept was an attempt to explain all the variety seen as something other than "New Information" and there were lots of examples tossed around, comparisons to hands of cards being different but still just a subgrouping of the original 52 cards.

The idea was of devolution where each succeeding generation would have less perfection, less of the original genetic material.

There is a similar version that uses a Super-Genome in a slightly different way, as something that drives Super-Hyper Speed evolution. This version says that all the life we see comes from evolution of the "Kinds" taken on the ARK. Well, to get what we see if there was an initial population of only two to seven of each kind requires evolution at a speed simply unimaginable.

But what Oetzi shows us is that things just weren't all that different even during the time Adam supposedly lived. There just isn't some Super-Genome or Super-Hyper Speed Evolution.


Aslan is not a Tame Lion
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jar
Member
Posts: 30934
From: Texas!!
Joined: 04-20-2004


Message 52 of 66 (436995)
11-28-2007 12:31 PM
Reply to: Message 49 by Hyroglyphx
11-28-2007 12:22 AM


Re: written in the Year 5767
Just to give you an example that just came up at EvC. In Message 42 Beretta posts:

Forget the modern banana and the original banana -they're all still bananas -perhaps with a little loss of information from the original -but noways is it going anywhere.

It is that idea that some original kind held all the information, had a Super Genome, that I am trying to address.

The facts are as Oetzi shows, there just plain ain't much difference between critters and plants from 6000 years ago and today. There was no Super Genome.

The facts are that bananas are part of the same order as ginger and arrowroot and cardamom and a host of other related plants.


Aslan is not a Tame Lion
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Equinox
Member (Idle past 3222 days)
Posts: 329
From: Michigan
Joined: 08-18-2006


Message 53 of 66 (437000)
11-28-2007 12:42 PM
Reply to: Message 49 by Hyroglyphx
11-28-2007 12:22 AM


Watch to see if this Creationist idea implodes in a few decades like so many others.
NJ wrote:

Who says there was a super-genome? Who made that claim?

(the discussion has partially answered this, but here is some more info)

The idea of a perfect super genome (PSG) followed by “degradation” after the fall is a late 20th century attempt by creationists to reconcile creationism with a raft of scientific evidence, such as speciation, the appearance of new traits in modern times, genetic disease, junk DNA, pseudogenes, and many more. The idea goes like this (but is altered if needed). First, 6,000 years ago, the created kinds had large, perfect, and super genomes, which included all of the “information” that would ever be contained in the genomes of any of their descendants. Then, starting at the fall, God allowed their genomes to degrade over time by mutation (note that these mutations can result in variations, and that these variations are heritable, however the variations must be considered “bad”, regardless of what they do).

This is invoked to explain all manner of phenomena like those mentioned above. Notably, the degradation is not linear, but can be precipitous within a few centuries after the fall, then very slow for millennia after, or whatever, as the creationist needs.

The PSG idea is very widespread – I’m a bit surprised that NJ or indeed any moderately read (not just well-read) creationist can be unaware of it. It’s proponents include most modern and large creationist groups, such as Answers in Genesis, Institute for Creation Research, Kent Hovind’s “Creation Science Evangelism”, Jehovah’s Witnesses, people like Wieland, Ham, Malone, and many more. In fact, I’m not aware of ANY large modern creationist movement or group (or even prominent individuat - perhaps Behe who admits our primate ancestors) that disputes it. Here are some quotes from modern creationists.

From Kent Hovind:

Creation predicts that although some life forms have degenerated and lost use of an original function, every part of an organism was designed to serve some useful primary or backup purpose.
http://www.drdino.com/articles.php?spec=9

From ICR:

If B. anthracis becomes a pathogen after acquiring two plasmids, how did these plasmids and amazing biochemical pathway of the toxins originate? As a reminder to the reader, creationists endorse a model of creation degrading under the effects of sin. Therefore, we may rephrase the questions above: Could the plasmids and toxins have degraded from something benign or even beneficial?
http://www.icr.org/index.php?module=articles&action=view&ID=312

From AIG:

It is simply unbelievable that these turtles could remain unchanged for over 100 million years, given that information-degrading mutations are known to accumulate in living things, generation after generation (a consequence of the Curse of Genesis 3).
http://www.answersingenesis.org/docs2005/0418turtles.asp Another at http://www.answersingenesis.org/creation/v24/i1/fouling.asp

As with many other creationist claims, the PSG is at least somewhat testable, and case after case (such as Otzi), shows that it’s complete rubbish. I’ll list some of those cases in a subsequent post, which will be copied from our earlier discussion of the PSG.

Have a fun day everyone-

Equinox

Edited by Equinox, : added bold


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Equinox
Member (Idle past 3222 days)
Posts: 329
From: Michigan
Joined: 08-18-2006


Message 54 of 66 (437002)
11-28-2007 12:48 PM
Reply to: Message 1 by jar
09-24-2006 2:39 PM


Many more clear refutations of the perfect super genome (PSG)
Such a general degradation across genomes, including both human and animal life (not to mention other kingdoms), should be detectable.
The most obvious thing to test are direct samples of ancient vs current DNA. While DNA does generally decay quickly, we do have samples that have survived. Here are some:

1. Neanderthal DNA. We have some Neanderthal DNA. While a number of dating methods put Neanderthal DNA to between 40,000 and 100,000 years ago (depending on the sample), creationists usually claim that Neanderthals are normal h. sapiens who died in or before the flood. If so, then they are at least 4,500 years old. Using the creationist number, they had only 20 to 1500 years of degradation, compared to 6000 for humans today. Thus their genomes should have only a tiny fraction of psuedogenes and junk DNA. To try some numbers, we need to know how degraded we are today. I don’t know what a creationist would say, but from the claims of people like Faith, I think they would say a high number, since they feel we have degraded a lot since the fall (otherwise it’s a pretty wimpy force of sin and death). So lets say we have only 40% of our good genome left. If that’s the case, then we’ve degraded 60% in 6000 years. If the degradation is linear (again, big guess), then that’s 1% loss every century. So a Neanderthal genome should have around 0 to 15% degradation.

Such a huge difference would jump out to any geneticist looking at Neanderthal DNA. Since numerous studies have been done on Neanderthal DNA, It must not be there. The researcher couldn’t hide it since other people have seen Neanderthal DNA, and more importantly, they wouldn’t want to, since such a find would gain them instant fame. Even if someone were willing to hide data if it favored creationism, they still wouldn’t hid this since it can be interpreted other ways.

2. DNA from other ancient animals. We have a huge amount of insects in amber from what creationists would consider pre-flood times. The same math from above applies here, as well as the same logic.

3. Frequency of disease in the fossil record. Many diseases leave visible signs in bones. Diseases have been shown in fossils across the board, regardless of age. I don’t know that a quantified study of diseased fossil frequency has been done, but since a degradation from the fall until now should show a big difference, such a trend should stick out like a sore thumb, and I’m sure it would have been found if there.

4. Spina bifida in Neolithic England. The barrows around Stonehenge and similar Neolithic religious monuments are dated to around 2,000 to 5,000 years ago. Thus they should have around half of the degradation we have. Note that creationists generally agree with those dates, since we have roman and other records showing that refer to them as past civilizations. The bodies in the barrows have a high proportion of Spina Bifida (a birth defect). If there has been degradation since the fall, then ancient birth defects should be much lower, not much higher.

5. Human age at death over the millennia. We have human fossils all over the ancient time frame, and the age of a human fossil can be estimated from bone growth and bone changes. These fossils do not show that ancient people lived to anything near the ages in Genesis. Instead, they show a steady life expectancy, with variation from time to time due to things like food supply. Of course, one could argue that the bone changes that we use to determine age at death simply happened later, which could explain it, but would require that kids lived to, say, 50 years and were still kids, which seems difficult on the parents.

6. Wooly mammoth frozen bodies. It has been shown that sperm frozen in animals who have been frozen whole is still potent even after a few years. This work has encouraged people to think about using frozen mammoth sperm or eggs to breed or clone a mammoth. The DNA of mammoths has been compared to modern elephants to find differences. If the degradation hypothesis is true, then the mammoths would show little degradation , and the elephants a lot as per the math above. Such a difference would again stand out like a sore thumb. No such difference has been found.

7. Dendrochronology. Dendrochronolgy, as we know, is the method of counting tree rings to look at their growth in ancient times. Tree ring series go back 10,000 years in some places (I haven’t heard how creationists explain this – maybe a good new thread topic). (Also – what do creationists say about the flying sword mentioned in Genesis 3? Where did it go? Why can’t any skeptic just go and look at it?) Anyway, with better health, trees are known to grow more, giving wider rings. If there has been a general degradation, then it would be easy to see this in the tree ring series, which would show better health in the past, esp 6,000 years ago). They don’t show this however – they show the same amount of health (with variation) today, 100 years ago, 1000 years ago, 3,000 years ago, 6,000 years ago, 9,000 years ago, etc.

Well, 7 is the holy number according to the numerology soothsayers of the Bible, so I’ll stop there. Just a little thought brings more of them to mind (such as how long kings lived in Chinese records, which go back 4,000 years). In all of these cases, it is possible to test the predictions of the degradation hypothesis, and the predictions don’t match the data. Maybe a good way to explain this is to say that God reached in and altered each piece of this evidence to deceive those he’s already decide to burn in hell, just as “Paul” says he would in 2thes2:11?

That’s not even mentioning the huge amount of DNA that has been examined from Egyptian mummies that are thousands of years old, or from even more ancient people like the iceman.

The iceman is an interesting data point in this discussion. He’s from around 5350 years ago (date established by a variety of dating methods and confirmed by dendrochronology), putting him only about 650 years after Adam’s creation. Adam lived to 930. Thus, he could have known Adam – hell, he could BE Adam! If not, then he could easily be a son or grandson of Adam with the long lifespans reported in Genesis.

We’ve obtained DNA from the iceman, and studied it. If it had the proposed hypergenome, then that would have been obvious. It didn’t – it was like our genome. In fact, genetic problems such as the ones around today were identified in it. Note that for all of the human diversity to come from the (genetically) 5 people on the ark, then there must still have been hyper genomes at least in some significant way at the flood. The iceman died nearly 1000 years BEFORE the flood. If anyone should show a hypergenome, it should be the iceman. Yet his body (and his DNA) is in most respects much like ours.

There are undoubtedly dozens more that one more versed in the field than I can readily think of.

Oh yeah, there is also Cheddar man (9K ya).

Take care-
Equinox


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Hyroglyphx
Member
Posts: 5622
From: Austin, TX
Joined: 05-03-2006


Message 55 of 66 (437055)
11-28-2007 5:35 PM
Reply to: Message 50 by Wounded King
11-28-2007 6:37 AM


Re: Origin of the 'super genome'
The idea was principally Faith's although I'm not sure if she coined the term and I doubt the idea was original with her. Randman occasionally put forward similar ideas and John Davison's prescribed evolutionary hypothesis basically relies on the existence of a super genome as well.

Okay, after reading your post, I see now what the "super genome" theory is all about. No, it definitely was not an invention of Faith's. A few creationists, like Hovind, advanced the theory that everything prior to the Fall was in its purest state, which accounted for why people lived in to the several hundreds and why everything was bigger.

According to the theory, everything is winding down, including the universe itself. And while the Big Crunch is probably an inevitability, based on thermodynamic law, it doesn't necessarily mean that beings were in better shape back then-- or if they were, that it wasn't necessarily attributed to a better genome.

Some other factors could include a better diet, cleaner air, cleaner water, far more exercise, etc.

This original genome would need to be much larger than a modern genome as it would have many redundant sequences which serve to provide much of the genetic diversity we see today in modern species.

I think one has to consider that a bigger genome wouldn't necessarily mean better. Besides, if our genome had less base pairs than it has currently, wouldn't that be absolutely catastrophic? We certainly wouldn't look like we do now, it seems to me.

So the simplest form would be a super genome which had sufficient genetic material to produce all the geneti diversity we see today.

I suppose theoretically there could be some validity to that, but currently there is nothing that would bring it out of anecdotal mode.

Does this clear the idea up a little?

Very much so, thanks.


“This life’s dim windows of the soul, distorts the heavens from pole to pole, and goads you to believe a lie, when you see with and not through the eye.” -William Blake
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Equinox
Member (Idle past 3222 days)
Posts: 329
From: Michigan
Joined: 08-18-2006


Message 56 of 66 (437560)
11-30-2007 2:13 PM
Reply to: Message 55 by Hyroglyphx
11-28-2007 5:35 PM


Re: Origin of the 'super genome'
NJ wrote:
A few creationists, like Hovind, advanced the theory that everything prior to the Fall was in its purest state, which accounted for why people lived in to the several hundreds and why everything was bigger.

Um, did you read my post #53 in answer to your question? The super genome is obviously not some splinter idea – I’m hard pressed to find ANY major creationist group that refutes it, and many that support it, such as ICR and AIG. Your line above “a few creationists” sounds like it’s a small minority. That doesn’t appear to be the case to me. You may of course be right, but do you have anything to suggest that the PSG isn’t the dominant view of YECs today? Or did I mishear you, and you aren't saying that PSG supporters are a minority?

The only other large creationist group I could think of was CRS, and a quick search of their site shows that they support it too:

The Creator has created time, space, matter, and life at once in all their complexity, whereupon the universe degrades gradually and continuously according to the second principle of thermodynamics. This is Biblical creationism.
(in an extended article that uses this to show that mutation degrades the genome, never the reverse. http://www.creationresearch.org/crsq/articles/37/37_3/Fertility.htm

NJ wrote:

Besides, if our genome had less base pairs than it has currently, wouldn't that be absolutely catastrophic? We certainly wouldn't look like we do now, it seems to me.

Pardon my bluntness, but how did you come to this conclusion? The majority of our genome (like other genomes) is garbage – gibberish, sections that serve only to copy themselves like chain letters, and whatnot. Sure, useful roles have been found for a small percentage of what was first called “Junk DNA”, but huge amount of Junk DNA appear to really be junk. The statement above seems to ignore the past 20 years of genetics research. Am I missing something?

I suppose theoretically there could be some validity to that [the PSG], but currently there is nothing that would bring it out of anecdotal mode.

I agree, based on the evidence we have. But by saying that, aren’t you saying that the majority of creationists today are simply being silly (at best)?

Thanks, and have a fun day-

Equinox


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jar
Member
Posts: 30934
From: Texas!!
Joined: 04-20-2004


Message 57 of 66 (439882)
12-10-2007 6:45 PM


Looks like the Super Genome may be coming.
Recent genetic studies seem to show that the Super Genome may be real, just not quite here yet, still to come.

According to this report, beneficial mutations in the human genome sped up around the time of the imagined Fall and are still continuing.


Immigration has been a problem Since 1607!
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sidelined
Inactive Member


Message 58 of 66 (439951)
12-10-2007 11:10 PM
Reply to: Message 57 by jar
12-10-2007 6:45 PM


Re: Looks like the Super Genome may be coming.
Jar

LOL Now I wonder how the fundies are going to spin the verbal diarrhea to convince the gullible that what they said about beneficial mutations was just misunderstood.


"Logic will get you from A to B. Imagination will take you everywhere."

Albert Einstein


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mobioevo
Member (Idle past 4024 days)
Posts: 34
From: Texas
Joined: 12-13-2007


Message 59 of 66 (440981)
12-15-2007 5:45 PM
Reply to: Message 50 by Wounded King
11-28-2007 6:37 AM


What is a super-genome
quote:
the ongoing degradation of several original created genomes. This original genome would need to be much larger than a modern genome as it would have many redundant sequences which serve to provide much of the genetic diversity we see today in modern species.

When I first came across this thread I was like, "WTF is a super-genome?" Now I get it. It is crazy how some people that don't understand something outright dismiss it instead of trying to understand the fundamentals of the problem, such as Faith did with radiocarbon dating.

Sorry if this is off topic, and if it is let me know. My question is why do creationists refuse the idea of genetic information being created? Do they only want some supernatural power to create all genetic information?


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mobioevo
Member (Idle past 4024 days)
Posts: 34
From: Texas
Joined: 12-13-2007


Message 60 of 66 (440989)
12-15-2007 6:13 PM
Reply to: Message 57 by jar
12-10-2007 6:45 PM


Re: Looks like the Super Genome may be coming.
I would be careful in accepting these recent findings. Their methods still need to stand up to debate.

There is another thread on this topic, Is Human Evolution Speeding Up. I linked to arguments to their results in that thread.


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