Southern Adventist University opens Origins Exhibit
@pauluc:

If I may summarize our previous posts on allelic variation, SNPs and speciation
You suggest

1] There was frontloading of genetic information in a breeding pair for most species 2349-2348 BC.

The frontloading was at the time of creation by the Creator (less than 10,000 years ago), with a genetic bottleneck at the time of the Noachian Flood some 4,000 or so years ago . . .

2] Variation leading to speciation within kinds was by genetic mechanisms of allelic variation from the original gene pool. Maybe 10-20% of the variation can be attributed to this front loading.

It depends what type of variation you’re talking about. All of the variation beyond very low levels of functional complexity is the result of frontloading . . .

3] Most of the allelic variation and SNPs seen in species today has arisen by random mutation within the populations derived from this starting population of 4 haplotypes. ie 80-90% of the variation within species derived from “kind” ancestor.

At low levels of functional complexity, yes, the vast majority of allelic variations are the result of random mutations.

4] Most (80-90%) of the phenotypic differences seen between species has occurred by natural selection and genetic drift.

Within the same basic “kind” of gene pool – yes.

5] Any differences due to RM/NS after selecting the front-loaded pair can only confer very very low level complexity.

That’s right.

6] There is a barrier of 1000fsaar that limits any ability to generate anything novel and complex within this 80-90% of new mutations.

Yes.

Apropos of the recent paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310774/?tool=pubmed

How do you modify your model of constraint by 1000fsaar to account for the role of SNPs in determining the effects of non-coding regulatory elements? In this context any discussion of hamming distance is really examining the edge effect of minimal relevance. I should not have to explain how this is particularly germane and impacts your discussion about genetics of feathers and the regulation of genes controlling feathered phenotype.

Non-coding regulatory elements are key to the building of complex systems within living things – far more important than are the protein-coding genes themselves (which function more like bricks and mortar that can be used to create many different types of buildings). SNPs can affect these regulatory elements, obviously. However, SNPs cannot affect these regulatory elements in a way that causes them to produce a qualitatively novel type of “building” with the “bricks and mortar” – beyond very low levels of functional complexity of course. In other words, you have to ask yourself the odds that a single point mutation to a regulatory non-coding sequence, or any other type of mutation, will result in a change in the location of the final product to an entirely novel island in sequence space that has a qualitatively unique function that requires a minimum of more than 1000 specifically arranged amino acid parts? That just doesn’t happen. There are no examples of this anywhere in literature – period.

If you would actually sit down and do the math, you’d see why. Sequence space has a fairly uniform distribution of potentially viable sequences/structures. As the minimum size and or specificity of the system under consideration increases in a linear manner, what do you think happens to the ratio of potentially viable/beneficial vs. non-viable/non-beneficial sequences in sequence space? The number of non-viable sequences increases in an exponential manner compared to the potentially viable sequences. The means that the viable sequences become more and more isolated in sequences space, dramatically so, with each step up the ladder of minimum size and/or specificity requirements. This means, of course that the minimum likely gap distance between viable sequences in different island clusters increases in a linear manner with each increase in the minimum size and/or specificity requirements. And, this means, of course, that the average time needed for any kind of random mutations needed to traverse the linearly increasing gap distances increases exponentially.

Now, tell me, how do you solve this sequences/structure space problem at increasing levels of functional complexity? Do you really not see the exponential nature of the problem? There is really no point in further discussion if you will not discuss this particular question. I really don’t understand your continued reluctance to substantive address such problems or consider the statistical basis for your own evolutionary assumptions. Why don’t you sit down and actually do a few calculations? Why not calculate the odds, for yourself, of any kind of mutation or series of mutations in any kind of coding or non-coding region evolving any kind of qualitatively novel system at various levels of functional complexity?

Give it a shot already. What could it hurt?

Sean Pitman
www.DetectingDesign.com

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Southern Adventist University opens Origins Exhibit
@pauluc:

Since you havent responded to my request to identify in the genomic comparison of mammalian species or primates with the instances of where the 1000fsaar criteria limiting the sequence differences, I suggest an alternative.

But I have responded to this question at least a couple times in this thread. Please go back and review these responses to you and Jeff Kent.

Please provide insights on this recent paper from Kate Sullivans group on Human Accelerated Regions that are proposed to be contributors to the differences between humans and Chimps particularly in limb and brain development. Im interested in the comparison between human SNPs and the varying presence of these SNPs in chimp, Neandertal and Denisova genomic sequences.

Differences between human and ape brain development are based on more than SNPs (which would produce quantitative differences in form and function, but not produce qualitative changes beyond very low levels of functional complexity).

As already noted a few posts above in this thread, humans and apes are quite different in various respects, to include brain structure and function – which is thought to be based on numerous differences in genetic regions that code for miRNAs (around 8% of which are human specific).

“miRNAs recently have been implicated in synaptic development and in memory formation. As the species specific miRNAs described here are expressed in the brain, which is the most complex tissue in the human body, with an estimated 10,000 different cell types, these miRNAs could have a role in establishing or maintaining cellular diversity and could thereby contribute to the differences in human and chimpanzee brain … function.”

Eugene Berezikov, Fritz Thuemmler, Linda W van Laake, Ivanela Kondova, Ronald Bontrop4, Edwin Cuppen & Ronald H A Plasterk, “Diversity of microRNAs in human and chimpanzee brain”, Nature Genetics, Vol 38 | Number 12 | December 2006 pp. 1375-1377.

The Y-chromosome is even more unique. A study published by Nature in early 2010 showed many striking differences between human and chimp chromosome structure, gene content, and even qualitatively unique genes between the two species.

As far as looking at specific genes, the chimp and human Y-chromosomes seem to have a dramatic difference in gene content of up to 53 percent. In other words, the chimp is lacking approximately half of the genes found on a human Y-chromosome. Because genes occur in families or similarity categories, the researchers also sought to determine if there was any difference in actual gene categories. They found a shocking 33 percent difference. The human Y-chromosome contains a third more gene categories, entirely different classes of genes, compared to chimps.

Hughes, J.F. et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure gene content. Nature. 463 (7280): 536-539.

For further discussion see:

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

I am sure you see P Troglodyes as entirely unrelated to man but I am a little unclear on your model of origins in terms of relatedness of Neandertal and Denisova hominids to man. Are they the children of Adam, Noah or neither? How do you account for any sharing of SNPs, the HAR and the development of pehnotypic differences by SNPs?

Neandertals and Denisova are human, descendants of Noah. They are simply ethnic variations of humans. Even mainstream scientists think that they could interbreed with each other to produce viable and virile offspring.

Of course there will be SNP differences between modern humans and Neandertals and other ancient ethnic groups – as there are between modern ethnic groups. And, these SNPs may be associated with functional differences – but not beyond low levels of functional complexity (usually only quantitative differences of the same basic type of gene function).

As far as the HAR-1 RNA, there are 18 character differences between humans and chimps (out of 118 characters/nucleotides). These differences are thought to play some role in the development of our brain differences, but no one knows exactly what role. Obviously, there are many structural and functional brain differences at high levels of functional complexity. However, there are also many unique non-coding genetic elements that seem to be involved with these differences (as already explained). No single point mutation or small cluster of mutations is going to be able to cross the gap between any qualitatively novel higher level system of function. Again, there are no examples of this in literature – for very good statistical reasons.

Another paper that cries out for your interpretation including the point at which ignorance about the 1000fsaar limit has blinded this group of scientist.

http://www.ncbi.nlm.nih.gov/pubmed/22398555

Critique below the abstract would be most helpful in seeing the errors.

Where in this paper is there any discussion of levels of functional complexity and how mutations can generate qualitatively novel systems at high levels of functional complexity? Remember, we aren’t just talking about quantitative differences in functionality here. We are talking about qualitatively novel differences beyond low levels of functional complexity. We need some actual math here – a few statistical calculations as to the odds that the just-so stories in papers like this might or might not actually be likely to be realized in a given span of time. Please do quote for me the relevant portion of this or any other paper along these lines.

Don’t just give me a bunch of references without any quotes or commentary (aka: reference mining). Show me that you actually understand the problem under discussion by, well, discussing it for a change with the use of quotes that you think are relevant. That would be most helpful…

Sean Pitman
www.DetectingDesign.com

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Southern Adventist University opens Origins Exhibit
@Professor Kent:

Again, the question is why does one accept the Bible among so many compete options as the real Word of God? If this choice is based on blind faith without any rational basis or appeal to the weight of empirical evidence, what you have is nothing much more useful than wishful thinking… not the kind of faith that has the power to provide a solid hope in the future for most rational people – especially in the face of very difficult trials or even the threat of torture and death.

What you’re asking people to do is to accept the Bible without really considering the weight of empirical evidence or any additional evidence that may contribute to the current weight of evidence for or against the Bible’s credibility. That’s simply not a rational expectation. Certain God does not expect anyone to believe without a rational basis for belief or faith set upon the weight of evidence that would appeal to the candid mind.

In this line, we are talking about what paid representatives of the SDA Church are teaching and/or preaching in the name of the Church. The Adventist Church, as an organization, simply cannot afford to pay people to go around teaching our young people that the best we have to support the Adventist position on origins is faith that is effectively blind to the otherwise overwhelming scientific basis for neo-Darwinism. That simply isn’t helpful to Adventism. Those who believe in neo-Darwinism, however honest and sincere they may be (and there are many in this category) cannot effectively represent the Adventist perspective on several fundamental doctrinal positions within our schools…

Sean Pitman
www.DetectingDesign.com

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Conrad Vine Continues to Attack Church Leadership
If the human immune system were the “perfect mechanism” that God originally designed it to be, you’d be right. However, after ~6000 years of sin and decay, the human immune system is no longer what God originally designed it to be – as evidenced by the great many, even among healthy vegan SDAs, who died during the pandemic. Water and light therapies are great and are helpful as layers of protection, but for many, especially those over the age of 65, whey were not enough. The mRNA vaccines were very effective in providing an additional much needed layer of protection during the pandemic. Now, I’ve very glad that you did not get sick enough to require hospitalization and that you avoided long-term injuries and death during the pandemic, but many many others were not so fortunate.

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Conrad Vine Continues to Attack Church Leadership
Yeah, I think you’re right…

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Conrad Vine Continues to Attack Church Leadership

Hi Sean,

Hope all is well.

I see you wrote a recent article defending the covid vaccine. You seem to be the main protagonist in the church championing the cause of the covid vaccines.

I am on the opposite spectrum

I personally did not touch any of those vaccines, and won’t ever either. I just see to many red flags and it’s alarming to me. Could you possibly explain to me what Revelation 18:23 speaks about please? I would love to hear your take on that verse.

Justin S

Hi Justin,

Thank you for your note. I do appreciate your concerns and your convictions. It can be very confusing to sort out so many different voices saying so many different things regarding what to think and what do to keep oneself as healthy as possible.

Regarding Revelation 18:23, in particular, the term “pharmakeia” is best translated as “sorcery” here. There is no intended advice at all against modern medicine in this passage. After all, would it be wise to suggest that medications like antibiotics to treat bacterial infections or insulin to treat diabetes are evil “sorceries”? Again, such arguments only make the Christians who say such things look sensational and irrational – which puts the Gospel Message itself into a bad light for those who are considering following Christ.

COVID-19 and Vaccines – Update

Consider also that Ellen White herself promoted various medications and medical therapies of her day that she considered to be helpful in various situations? – to include the use of what was generally regarded as a “poison”, quinine, to prevent malarial infections for missionaries who worked in malaria-infested regions of the world? She wrote, “If quinine will save a life, use quinine.” (http://www.educatetruth.com/featured/the-arguments-of-adventists-opposed-to-vaccines/#Ellen-White-and-the-Smallpox-Vaccine) She also supported the vaccination of her son William, both as a child and as an adult (despite William having had an adverse reaction to vaccination as a child) (http://www.educatetruth.com/featured/the-arguments-of-adventists-opposed-to-vaccines/#Ellen-White-and-the-Smallpox-Vaccine). She supported blood transfusion when necessary, despite their risks (https://text.egwwritings.org/publication.php?pubtype=Book&bookCode=2SM&lang=en&collection=2&section=all&pagenumber=303). And, she even supported using radiation therapy when appropriate, despite its risks (https://text.egwwritings.org/publication.php?pubtype=Book&bookCode=2SM&lang=en&collection=2&section=all&pagenumber=303). Beyond this, she recognized the advantages of anesthesia during surgery and the use of medicines to relieve the intense pain and suffering of the injured or sick (https://text.egwwritings.org/publication.php?pubtype=Book&bookCode=2SM&lang=en&collection=2&section=all&pagenumber=286&QUERY=before+major+surgery&resultId=1&isLastResult=1).

I hope this helps you at least understand why I take the position that I take. I mean, I’m a pathologist with subspecialties in anatomic, clinical, and hematopathology and have studied COVID-19 and the mRNA vaccines in great detail. Beyond this, I’ve seen the results myself, with my own eyes – and so has my brother-in-law, pulmonologist Dr. Roger Seheult who runs a large ICU in S. Cal. We’ve seen ICUs overflowing, beyond max capacity, with the very sick and the dying during the height of the pandemic – the vast majority of whom were unvaccinated. Roger’s face and hands are the last things that many saw and felt on this Earth. It was very personal for us. We were actually direct eyewitnesses. And, we’re not alone. This very same situation was happening all around the world during the pandemic. Truly, the mRNA vaccines saved millions of lives and prevented many many more hospitalizations and long-term injuries.

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Conrad Vine Continues to Attack Church Leadership
Regarding Mandates:

“While the available data in 2021 and early 2022 suggested that being vaccinated conferred tremendous personal benefit to the recipient, such that it was unclear if there could be added gain for demanding others be vaccinated too for added protection. By mid-2022, vaccines did offer modest reduction in transmission, but personal health benefits against severe disease were largely retained. Yet, by the fall of 2022, with the emergence of the Omicron variant, a new verdict had emerged. Vaccines were unable to halt transmission in the presence of escape variants; thus, here too, mandates failed to meet the ethical pre-requisite of benefit to others, as a vaccinated person could still spread the virus. A study in the New England Journal of Medicine showed comparable rates of viral shedding comparing vaccinated to unvaccinated people with COVID-19 (Boucau et al. 2022).” (Vinay Prasad, 2024) 

I was never personally a fan of the vaccine mandates put out by the US government (or other governments around the world) since they seemed to me to be largely counterproductive and provide little benefit regarding limiting the spread of the virus after the Omicron variant came out. As Dr. Prasad points out here (Link), the mRNA vaccines were so good as far as personal protection was concerned, that limiting the spread of COVID-19, once the vaccines became available, was kind of a moot point.

That being said, once the government mandates were in place, I also didn’t see it as appropriate to claim religious liberty as a reason for refusing to get vaccinated – since there is nothing in the Bible that would prevent one from obeying a government mandate along these lines (Link). People often cite the case of Daniel and his three friends refusing the king’s meat as a Biblical basis for refusing to comply with vaccine mandates. The problem here is that the vaccines themselves were not unhealthy or unreasonable during a pandemic and their use was not recognized as a form of idol worship. Also, Daniel’s proposed 10-day test would not have had the same results with respect to the mRNA vaccines, but would have shown benefits for the significant majority of people.

As Ellen White put it:

“In cases where we are brought before the courts, we are to give up our rights, unless it brings us in collision with God. It is not our rights we are pleading for, but God’s right to our service.” (Ellen White, Manuscript Releases 5:69 – 1895)

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Conrad Vine Continues to Attack Church Leadership
Wow! I had no idea.

However, this does seem to be inconsistent with the following on Canadian Law regarding Religious Liberty (from the 1982 Canadian Charter of Rights and Freedoms):

Sincerity of belief is a question of fact. To establish sincerity, an individual must show that they sincerely believe that a certain belief or practice is required by their religion. The religious belief must be asserted in good faith and must not be fictitious, capricious or an artifice. In assessing the sincerity of the belief, a court will take into account, inter alia, the credibility of the testimony of the person asserting the particular belief and the consistency of the belief with that person’s other current religious practices (Multani, supra at paragraph 35; Amselem, supra at paragraphs 52-53). It is the sincerity of the belief at the time of the interference, not its strength or absolute consistency over time, that is relevant at this stage of the analysis (R. v. N.S., [2012] 3 S.C.R. 726 at paragraph 13).

The Court does not want to engage in theological debates when examining the practice or belief in question. The practice or belief in question need not be required by official religious dogma nor need it be in conformity with the position of religious officials. Freedom of religion extends beyond obligatory doctrine to voluntary expressions of faith and is not restricted to major and recognizable religions (Amselem, supra at paragraphs 46-50, 53, and 56). A protected religious practice need not be part of an established belief system or even a belief shared by others. An individual need only demonstrate a sincere belief that the practice is of religious significance to the individual (Little v. R., 2009 NBCA 53, leave to appeal dismissed, [2009] S.C.C.A. No. 417 at paragraph 7). It is not appropriate to adduce expert evidence showing sincerity or lack thereof (Amselem, supra at paragraph 54).

https://justice.gc.ca/eng/csj-sjc/rfc-dlc/ccrf-ccdl/check/art2a.html

So, given the above, are there any examples were someone actually was able to present so-called “objective” evidence in the form of a “tenet of religious faith”, which actually achieved success? where such an individual would not have been fired? I mean, let’s just say, for argument sake, that the Catholic Church had a fundamental tenet of faith which opposed vaccinations. Would this really have made a difference in Alberta for members of the Catholic Church? Would these people have been allowed to keep their jobs while all other vaccine objectors lost theirs? – despite the statements above suggesting that personal religious belief and liberties are not dependent upon that of an established belief system?

It’s not that I’m opposed to mandated civil laws in an effort to maintain public safety/health. For example, various kinds of jobs require one to be follow various personal health regulations – like working in the hospital or performing surgeries while masking and wearing sterile gloves and taking various vaccinations. There are also quarantine laws that are quite reasonable in various situations/settings. That being said, great efforts should be made to support personal religious/moral convictions as long as such support does not significantly interfere with the liberty and/or safety of others.

Any suggestions on any potential improvement of the wording of the SDA position on vaccines or other modern medical therapies and/or religious liberty statements?

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