@BobRyan: I heard recently that the problem of genetic mutation …

Comment on Wisbey talks about LSU and what he wants you to know by Sean Pitman.

@BobRyan:

I heard recently that the problem of genetic mutation argues for young life on earth because the harmful mutation rate is much faster than previously supposed. In each generation Children have something like 100 mutations not found in their parents.

The mutation rate is more like 200-300 per person per generation. This mutation rate is far too high to avoid eventual extinction through the inevitable build up of detrimental mutations within the gene pool. For a detailed discussion of this problem see:

http://www.detectingdesign.com/dnamutationrates.html

Sean Pitman
www.DetectingDesign.com

Sean Pitman Also Commented

Wisbey talks about LSU and what he wants you to know
@Geanna Dane:

Sean, given your understanding of changes in what we view to be functional DNA, perhaps you would find agreement with the following statement from Armin Moczek (Current Topics in Developmental Biology 86:135-162, 2009):

“Novel traits do not require new genes or developmental pathways to come into being, but instead may arise from co-option of pre-existing developmental machinery into new contexts”.

This is the party line, but it just doesn’t happen beyond very low levels of functional complexity and statistically it is extremely unlikely to happen this side of a practical eternity of time. What is known about the nature of sequence/structure space, and the exponential decline of potentially beneficial vs. non-beneficial, removes the scientific tenability from such assertions…

To say that macroevolutionary changes are impossible is a claim that exceeds what is known and relies strictly on faith. And that’s okay so long as one does not use science, which is far from complete on the topic, to back this claim. However tempting the argument from ignorance may be, it is simply inappropriate. Of course, to say that macroevolutionary changes are possible also represents an assumption that cannot be validated by science and requires faith, but it leaves open possibilities that can be studied by science–which contrasts sharply with the position of the macroevolution denier.

Science is all about what is “most likely” given what is known right now – not what might be known in the future. And, given what is known right now, functional evolution beyond very very low levels of qualitatively novel functional complexity (systems that require a minimum of more than 1000 specifically arranged residues) doesn’t happen and is in fact statistically unlikely to happen this side of trillions upon trillions of years of time.

To suggest that this information is not actually available shows an ignorance of the available information regarding the nature of sequence/structure space at various levels of functional complexity.

Before dissecting this statement, please bear in mind that one cannot prove a negative (other than things like a mathematical term or a chemical charge). One cannot prove that a volcano never erupted at the present-day site of the U.S. capital. One cannot prove that bigfoot (the big hairy ape of North America) does not exist today. One cannot prove that Abe Lincoln never told a lie.

And one cannot absolutely prove that Stonehenge isn’t really just a natural rock formation, or that sickness isn’t really the result of voodoo. No one can prove that garden fairies, the Flying Spaghetti Monster, or Santa Claus don’t really exist. Yet, no one (but children perhaps) believes that they do. Why not?

This is the argument of those like Dawkins and Provine who argue against the practicality of believing in a God that offers no positive evidence of His existence. Are they right to suggest that such a “faith” is equivalent to believing in the Flying Spaghetti Monster?

The same thing is true of the faith of scientists in the creative potential of RM/NS beyond very low levels of functional complexity. There is no positive evidence for such faith regarding the creative potential of this particular mechanism beyond very very low levels of functional complexity. Nothing along these lines is observable or even statistically tenable. Where then is the “science” behind such assertions? Where is the calculable predictive value? Where is even the potential for testable falsification?

What does have predictive value is that such evidence is very unlikely to be discovered given our past history of experience with the available data. The positive evidence describing the nature of sequence space should be overwhelming to the candid mind regarding the likelihood of discovering something equivalent to garden fairies.

Therefore, the “proof of a negative” is the lack of evidence to the contrary – after extensive investigation.

Can I absolutely prove that someone winning the California Lottery 100 times in a row didn’t do so by pure chance? that no deliberate design or cheating was involved? No. I cannot absolutely prove a negative as you point out. However, does this then mean that chance is the best scientific explanation for such a series of events? – that there is no reliably determinable scientific alternative explanation?

You’ve just illustrated a basic limitation of science – that nothing is absolutely provable by science. There are only degrees of certainty in science. Nothing is absolute. There isn’t even absolute positive evidence in science since everything must be subjectively interpreted with potentially falsifiable theories…

Personally, I don’t believe we will have good answers until we learn while sitting at the knee of Jesus. I can live by faith until then.

There are many things we won’t know till then. However, this does not mean that God hasn’t given us abundant evidence right now – scientifically viable evidence of His existence and the reliability of His Word, revealed will for our lives, and a solid scientific basis for a bright future that He has promised.

Without this evidence I don’t see your faith as being more attractive to me, if I had no other information, than a faith in Santa Claus or garden fairies or Dawkins’ Flying Spaghetti Monster. I’m sorry, but blind faith based on warm fuzzy feelings and nothing more just doesn’t do it for me when it comes to thinking that I will ever actually sit at the real physical feet of Jesus someday…

Sean Pitman
www.DetectingDesign.com


Wisbey talks about LSU and what he wants you to know
@David Read:

Geanna, regarding the clock running down, it is an inference that can be made based upon what is known. One thing Sean mentioned is that given the rate of mutation observed today, the human race should be extinct if it is really around two hundred thousand years old. A reasonable inference is that in past, the rate of harmful mutations was lower and has increased as time has gone on.

There really isn’t any known “reasonable” way to hypothesize a significantly reduced mutation rate in the past compared to today (i.e., around 200-300 mutations per individual per generation). The reason for this is because the basis of most mutations is known. The error rate of DNA transcription is known as well as the repair rate. The combination of these two rates produces a final mutation rate. This final mutation rate would be very difficult to significantly reduce given the nature of the transcription and repair proteins. There would have to have been some other mechanism of error detection and/or repair in order to significantly reduce the mutation rate in the past.

I’m not an expert in the molecular genetics, but the genome of humans and most species contains a very high percentage of non-coding DNA once termed “junk DNA.” Much of this code may have been functional in the past, but no longer is.

This is no longer true. The assumption that non-coding DNA is truly non-functional or “junk” is an evolutionary assumption that has recently proven false.

It is actually a creationist prediction that non-coding DNA would be found to be functional. It is very interesting, therefore, that non-coding DNA, to include many “pseudogenes”, pyknons, repetitive sequences, and the like, have proven not only to be functional, but vitally functional – even more functional that the genes or “coding” sequences themselves. The genes are like the basic bricks and mortar of a house while the blueprint as to how the bricks and mortar are arranged, as to what type of house is built, is within the non-coding DNA.

For example, pseudogenes appear to be genes that were once functional but became non-functional as a result of mutations. Another example is the abundance of mobile genetic elements like transposons and retroviruses, which hint that, in a period in the past, the genome was far more flexible and amenable to useful and rapid change and modification. If the genome were studied with the assumption that “the clock is running down” rather than with the assumption that functionality and complexity are increasing through random replication errors, it would be much easier to understand and make sense of.

Again, many pseudogenes, mobile genetic elements and even retroviral sequences are being found to have beneficial functionality within the genome. While I agree with your conclusion that the original gene pool very likely had greater functional potential regarding quality and potential for diversification, your contention that much of the genome is non-functional evolutionary garbage doesn’t seem to be true.

Consider the following recent discoveries along this line:

No one knows yet just what the big picture of genetics will look like once this hidden layer of information is made visible. “Indeed, what was damned as junk because it was not understood may, in fact, turn out to be the very basis of human complexity,” Mattick suggests. Pseudogenes, riboswitches and all the rest aside, there is a good reason to suspect that is true. Active RNA, it is now coming out, helps to control the large-scale structure of the chromosomes and some crucial chemical modifications to them—an entirely different, epigenetic layer of information in the genome.
In fact, the most detailed probe yet into the workings of the human genome has led scientists to conclude [as of June 14, 2007] that a cornerstone concept about the chemical code for life is badly flawed. Reporting in the British journal Nature and the US journal Genome Research on Thursday [June 14, 2007], they suggest that an established theory about the genome should be consigned to history.
In between the genes and the sequences known to regulate their activity are long, tedious stretches that appear to do nothing. The term for them is “junk” DNA, reflecting the presumption that they are merely driftwood from our evolutionary past and have no biological function. But the work by the ENCODE (ENCyclopaedia of DNA Elements) consortium implies that this nuggets-and-dross concept of DNA should be, well, junked.

The genome turns out to a highly complex, interwoven machine with very few inactive stretches, the researchers report. Genes, it transpires, are just one of many types of DNA sequences that have a functional role. And “junk” DNA turns out to have an essential role in regulating the protein-making business. Previously written off as silent, it emerges as a singer with its own discreet voice, part of a vast, interacting molecular choir.
“The majority of the genome is copied, or transcribed, into RNA, which is the active molecule in our cells, relaying information from the archival DNA to the cellular machinery,” said Tim Hubbard of the Wellcome Trust Sanger Institute, a British research group that was part of the team. “This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed.”
Francis Collins, director of the US National Human Genome Research Institute (NHGRI), which coralled 35 scientific groups from around the world into the ENCODE project, said the scientific community “will need to rethink some long-held views about what genes are and what they do.”

ENCORE Project Consortium et al., Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature 447, 799-816 (14 June 2007); Richard Ingham, Landmark study prompts rethink of genetic code, Yahoo News, accessed June 15, 2007

“We fooled ourselves into thinking the genome was going to be a transparent blueprint, but it’s not,” says Mel Greaves, a cell biologist at the Institute of Cancer Research in Sutton, UK. Instead, as sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set — a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary….
“It seems like we’re climbing a mountain that keeps getting higher and higher,” says Jennifer Doudna, a biochemist at the University of California, Berkeley. “The more we know, the more we realize there is to know.”…
Researchers from an international collaborative project called the Encyclopedia of DNA Elements (ENCODE) showed that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA. Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. “Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive,” says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia.

Erika Check Hayden, Human genome at ten: Life is complicated, Nature 464, 664-667, Published online 31 March 2010

For a more detailed discussion of “pseudogenes” and “non-coding” DNA, see the following essay on my website:

http://www.detectingdesign.com/pseudogenes.html

Sean Pitman
www.DetectingDesign.com


Wisbey talks about LSU and what he wants you to know
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