Bill Basener (a participant here) co-authored a paper with John Sanford. He was given the honor of delivering a KEYNOTE ADDRESS at an international SECULAR biology conference. A video of his presentation is available in a link inside my write up of his presentation below. He alluded to some of the helpful input from his critics at TheSkepticalZone in his talk:
http://crev.info/2018/07/keynote-speech-falsifies-darwinism/
John Sanford is sort of the “Papa John” of creationist genetics. It is customary for the leader of a research group to be listed as the last author in a publication. That convention is seen in a variety of papers and books such as Rupe & Sanford; Basener & Sanford; Carter, Lee & Sanford; Montanyez, Fernandez, Marks & Sanford; and let’s not forget the Legendary High Velocity Team of Klein, Wolf, Wu & Sanford that permanently ensured the infusion of intelligently designed genes into a sizable fraction of Genetically Modified Organisms on planet Earth.
And perhaps one day in the distant future there will be a paper, “Cordova & Sanford”! 🙂
Below is a link of a paper from Papa John’s team about Adam and Eve which will be presented this week, July 29,2018 – August 1, 2018 at the 8th International Conference on Creationism
http://www.creationicc.org/2018_papers/15%20carter%20Y%20chromosome%20final.pdf
The existence of a literal Adam and Eve is hotly debated, even within the Christian body. Now that many full-length human Y (chrY) and mitochondrial (chrM) chromosome sequences have been sequenced and made publicly available, it may be possible to bring clarity to this question. We have used these data to comprehensively analyze the historical changes in these two chromosomes, starting with the sequences of people alive today, and working backwards to the ancestral sequence of the family groups to which they belong. The analyses of the chrY and chrM histories were done separately and in parallel. Remarkably, both analyses gave very similar results. First, the pattern displayed in both datasets supports a massive expansion of the human lineage, with multiple new branches forming from closely related individuals. Second, for both chromosomes, the mutation rate along each branch has not been the same through time. Third, both phylogenetic trees display a starburst pattern that centers around specific historical individuals, nearly all of whom lived in the Middle East. Fourth, we can know with a very high degree of confidence the actual sequences of the historical individuals that gave rise to each branch in both family trees. Fifth, within a reasonable margin of error we can approximate the sequence of Y chromosome Adam/Noah and Mitochondrial Eve. Sixth, given a few reasonable assumptions, we can estimate the time to Y Chromosome Adam/Noah and Mitochondrial Eve. Both individuals lived less than 10,000 years ago, which is most consistent with a biblical timeframe. Lastly, recurrent mutations are extremely common, and many of them are associated with epigenetic CpG sites, meaning mutation accumulation is not free of environmental influence and many mutations may have accumulated in different lineages in parallel. The genetic evidence strongly suggests that Y Chromosome Adam/Noah and Mitochondrial Eve were not just real people, they were the progenitors of us all. In this light, there is every reason to believe that they were the Adam/Noah and Eve of the Bible.
NOTE: Paul Nelson’s family was instrumental in the founding of the International Conference on Creationism which meets every 5 years. Paul is one of the few ID proponents openly associated with YEC. Nelson gave the 2013 ICC Keynote Address on Orphan Genes.
YECism is so bizarre.
Sal:
No harm in that, I guess, given the damage that Sanford has already inflicted on his scientific reputation.
Sounds like a bogus conference to me, the equivalent of a pay-to-publish online journal. Real conferences tend to be associated with some scientific society or other, e.g. SSE, AAAS, etc.
As for the abstract, there is much that is true and novel in it, but what is true is not novel and what is novel is not true. And I see that there is no mention of any genes with more than 4 alleles conserved between humans and chimps.
I’ll see Carter and Sanford tomorrow. If I remember, I can ask. If you have other objections, I’d be glad to hear them.
I’d certainly like to know how looking at exactly two linkage groups can tell you that two particular people are the exclusive ancestors of us all. I would also like to know how Noah, even if you assume the silly Ark story is true, could be the single male ancestor of us all. Didn’t the fathers of Noah’s and his sons’ wives contribute any autosomal loci to our ancestry?
John,
Thank you for posing some very good objections. Beyond, the meeting, these are questions I’ll try to keep on the table. If you come up with anymore, even long after the meeting, this thread would be a good repository for some of them.
I thought your allele objection was excellent and something the YECs on the whole must address. Thank you.
Of course the obvious objection is that YEC is ridiculous on many levels much more fundamental than any notion of coalescence within human genetics. Anyone trying to take it seriously must first deal with all those more fundamental objections: all the evidence for deep time, the geological and fossil records, phylogenetics, absence of global flood, incoherence of the Genesis stories and their mutual incompatibility, etc.
Its really cool and progressive to see papers based onbresearch that accuaret;y sees a option for two original people as the source pf mankind. This from the witness of God called the bible.
i went into the legend high velocity team thing but saw no relevance to ID/YEC. or possibly anything of note in science.
Anyways.
The problem with dna extrapolation concepts is that the DNA of Adam/Eve was that of people made to live for ever.
At the fall it was crazy screwed up to allow death. in their cases after hundreds of years. DNA of all biology , as a option, was open to interference by mechanisms we know nothing about.
I seriously question using DNA top draw conclusions about origins.
Sal,
YEC is difficult to defend but not impossible as a lot of things in the old universe and even OEC are assumed… On the other hand Darwinism needs the universe and the Earth as old as possible as D. Axe’s experiments show Darwinists need the universe older then 90 billion years old to explain the evolution of few proteins…
I’d still go with the universe older than 6 000 years…
Byers,
Yes, why pay attention to scientific evidence when we have the word of Jebus hisself?
I’m interested in hearing what you think “Jebus hisself” had to say about origins.
I think Harshman is referring to a well established scientific method of establishing the scientific facts that have proven the genetic differences in modern inhabitants of Paris who share an average of 50 per cent of their genes with people from Baghdad…
The same scientific methods have also shown that humans share 50 per cent of their genes with a banana…
Are the residents of Paris or Bagdad bananas? Or is Harshman and his bullet proof scientific method of establishing the genetic ancestry?
You are spouting factoids you don’t understand. I would suppose that what your factoid says about Paris and Baghdad refers to a proportion of highly within-species polymorphic SNPs, or something similar. What it says about humans and bananas, on the other hand, would be genes with recognizable homologies. If you don’t know what either of those is, that would more or less prove the point given in my first sentence. But it’s enough that you know that those two “50%” measures are not at all the same thing and are not comparable. Parisians and Baghdadis share 100% of genes with recognizable homologies; humans and bananas share 0% of highly within-population polymorphic SNPs.
“within-population” is a key term there J-mac. Just think about it.
Robert Beyers has been on the record on some forum stating that he supports a kind of post-floot hyperevolution with common descent at a level of some rather wide taxonomic ranks. For example, he thinks whales evolved from terrestrial mammals post-flood. But y’know, evolution is impossible and there are no transitional forms.
Somebody in this thread is definitely bananas.
Not saying who …
It’s curious to see someone being congratulated for making fools out of themselves and others.
Salvador making a fool out of himself finishes thus:
1. The articles cited refer only to the human genome (for very good reasons).
2. The very good reasons is that we have eliminated a lot of purifying selection from our population, which results in the spread and abundance of deleterious mutations, and thus, in their potential recombination, with obvious consequences.
3. We could evolve in the first place because of purifying selection.
This is a typical creationist maneuver. Take some studies out of context, make sure not to let anybody understand what’s really going on, and then conclude with grandiose fanfare that your fantasies about magical beings in the sky are true, while evolution is false.
Did you not recognize it? This OP is a mirror image of the posts by Tom English:
Fisher’s-Not-So_Fundamental_Theorem
and
Felsenstein presents the 37th Fisher Memorial Lecture
Compare that to the header and first paragraph of this post:
Sal is a just a sucker for that stuff.
Corneel,
Ha!
The most hilarious thing is Sal’s description of himself on that website. Just, LOL.
Still waiting…
I agree.
We find the same problem with nonhuman species.
I think the idea that genotype maps exactly to phenotype and that species are defined as genetically isolated populations is outdated.
Instead of looking for the genetic signature of Adam and Eve we should be looking for the cognitive, behavioral and anatomical features that separate them and us from the rest of the animal kingdom.
peace
Please tell that to all the IDers who use the “complex information” in DNA to infer design.
There is a category difference between looking for design in DNA and looking for precise species boundaries in DNA.
How can you not see that?
peace
You are right that there is a difference. Using DNA to cross-check phylogenic trees is science. Inferring intentional design is religiously motivated pareidolia.
Do you actually think using DNA to search for the founding pair in a particular species is equivalent to cross-checking phylogenic trees?
peace
From:
http://www.creationicc.org/2018_papers/15%20carter%20Y%20chromosome%20final.pdf
For an larger view:
http://theskepticalzone.com/wp/wp-content/uploads/2018/07/y_chromosome.png
In the above diagram, why is one branch length so looooong?????
The mitochondrial chromosome analysis.
The shape of the graphs is similar between Ychr and Mchr phylogenies.
Click for enlarged image of the Mchr phylogeny:
http://theskepticalzone.com/wp/wp-content/uploads/2018/07/mchr.png
Trying to make sense of the diagram. Help me, John Harshman, you’re my only hope.
The center of the diagrams is the supposed ancestor right? Now we have some poor chaps or gals that have lots more mutations than others relative to their common ancestors. Right? Wrong? Maybe?
No. See the place where it says “The small arrow denotes the approximate position of the evolutionary root”? That arrow is the root, which is what you mean by “supposed ancestor”.
Not at all to the degree you assume when you mis-locate the root. There are of course some branches that are somewhat longer than others. If most evolution is neutral, that’s because the long branches have more mutations. And there are various suggested reasons for variation in neutral mutation rate. There are also reasons for variation in non-neutral evolutionary rates, and those don’t involve difference in mutation rate.
Thank you for your input. First off, I made a mistake in my wording and should have explained the arrow. That fault lies with me.
The MEGA program that generated star diagram (or whatever you call it) doesn’t have the arrow put in it.
I believe Rob Carter put the arrow to show where the evolutionists place the root (out of Africa). The “true root” according to the MEGA/NJ reconstruction is the where all the branches converge right? Thanks again for your help.
In response to some of your very good objections, over breakfast with Rob Carter and dinner with Nathaniel Jeanson, here are some quasi-unofficial responses. I told them I would be trying to pass on their responses for discussion as I felt it important since people like me will either promote and defend their paper, and if they are wrong, I think they would want to fix it since they fundamentally their case is defensible minus a few mistakes if any…
The problem of conserved alleles between chimps and humans. The first issue is Both Carter and Jeanson adopted a convention I don’t use nor do I see used much. They go down to the nucleotide level and max out the possibilities at 4 per nucleotide (a,c,g,t).
Ok, something I don’t understand. Can genes mix parts and make a new allele occasionally during homologous recombination?
Carter’s solutions:
1. desgined ovum and sperm that have alleles than the somatic cells of Adam and Eve. I found that problematic philosophically and I think Jeanson does too.
2. mutations not random.
3. Frequency of those alleles (standard definition, not Carter and Jeanson’s) above 4 conserved between human and chimp should be rare.
4. many in CpG sites, so mutations biased, not random, but will tend to repeat across species.
Sanford, at his talk at the conference believed the designed ovum and sperm in adam and eve solved the linkage problem. I didn’t even need to pose the question since he said something to the effect, “evolutionists will complain about linkage.”
Regarding linkage, Jeanson laid out math at the dinner table which I didn’t understand, but said the linkage problem isn’t a problem.
So, some stuff made sense, some didn’t. In any case it’s an opportunity to study genetics.
Thanks again in advance for your responses.
No. That’s what “unrooted” means. There is no root intended or implied.
Thanks. I’ll have to raise the issue with Rob. I think that’s a good objection. Much appreciated.
A good objection to what? And you’re saying all these biology superstars don’t know this already?
Yes, they can. But how does this fix the problem that the alleles are the same ones chimps have? Coincidence? Divinely ordained recombination to fit?
Well,
AFAICT There is no need to “fix” this problem
The two species have a very similar phenotype. That is obviously true whether there is a common ancestor or not.
It seems pretty simple and uncontroversial to me. What am I missing?
peace
No, but I suspect they think (as I do), “rooting” a tree is usually bogus and driven by pushing a pre-determined narrative. That unrooted tree, as Carter discussed in his talk, is unprejudiced data, not to mention, some of the sub branches we have info on migrations and population structure.
Your stuff about evolutionary rates is bogus as illusutrated by the effect of changes in DNA repair mechanisms. And Carter pointed out the population structure can change the amount of mutations. How the heck can you guys ever calibrate molecular clocks over millions of years? Did you see what happened in Lenski’s experiments when a DNA repair mechanism failed? It’s nonsense to invoke molecular clocks over buzillions of years when they are subject to such extreme variation in the short term and in such a way that might not be corrected by a larger sample size over time.
The differences between species were there mostly by design, not mutation since there are barriers to common descent which you readily ignore starting with the Eukaryote/Prokaryote evolutionary questions.
The unrooted tree seems the least prejudicial in the absence of any other data. The way I see you evolutionists root the tree is with rather arbitrary decisions to give you the narrative you want.
So, when Rob isn’t busy and I have a chance to have discussion with him over it, I’ll mention the issue about unrooted trees.
Nevertheless, you raise good objections, but the “unrooted” issue is probably your lamest since it could be just as well be labeled “unprejudiced” in absence of any other data.
Your other objections, however, are very substantive and other creationists at the conference have echoed some of your objections, including me.
You other objections, however, are very bogus.
Sal,
At least some mutations have to be random, such as deleterious mutations…
But if most mutations are not random, as they appear to be, where is the additional information coming from in say a beneficial mutation that increases the fitness of an organism?
Are you familiar with the second law of thermodynamics that states that information can’t increase in the closed system?
Actually I’m the leading ID thinker on the 2nd law and it’s relation (or absence thereof) to ID. 🙂
I fancy myself as the leading thinker since I’m one of the few ID proponents who have vociferously argued that it’s a bad idea to use the 2nd law to defend ID. There are better arguments for improbability than the 2nd law.
My thoughts are here (minus a few arithmetic mistakes):
and
Sal
LoL. If by “second law of thermodynamics” you mean “coin tossing.”
You are missing the subject: supposed evidence for a bottleneck in the human population.
Yup.
As I understood (or misunderstood), if even making an evolutionary assumption and there is large diversity in the nuclear genome (male and female), but we have a bottle neck of two individuals (adam and eve, whatever), the mtDNA will have only a single copy for a while, but there will be diversity in the nuclear DNA if we allow for expansion of the population after the bottle neck. Unfortunately this does not absolutely rule out other explanations.
Jeanson had problems with my characterization, and I expect Carter and Sanford too. That’s ok, we can disagree and go back to the drawing board.
Whatever objections, even if proven valid, to Carter, Lee, and Sanford I think the approximate shape of the Y and the mtDNA NJ trees looks similar.
Carter argues the unrooted NJ Trees suggest a bottleneck. I agree with him. Yeah, unrooted trees aren’t supposed to imply what the common ancestor looked like, but to me, that’s about the best reconstruction possible. Carter at his talk said, “if 99% of the individuals on Earth have an A at one position and 1% a T, that suggests the common ancestor had an A.” That seems reasonable to me and hence justifies an interpretation of the unrooted tree the way Carter described it. He also argued some of the branches had reasonable traceable historical records associated with them such as the migration during the slave trade before the civil war, etc.
Hence, the long branch has lots of mutations in it relative to the common ancestor, and the molecular clock is likely broken not just because of possible DNA repair mechanism breakdown, but also because of population structure, etc.
Bottom line, creationism aside, I think he made a good case for a bottle neck followed by rapid expansion of population and geogrpahic dispersal.
stcordova,
“Why all this obsession with reducing entropy to increase design complexity? I hope one can see it can be desirable to INCREASE entropy (both design and thermodynamic) in order to increase design complexity. A warm living complex human has more thermodynamic and design space entropy than a dead lifeless ice cube”.
Just to clarify: does entropy in this context mean information?
stcordova,
Sal,
Can you recollect whether anybody has ever mentioned in the bottleneck debates that Adam and Eve, and possibly all the generations up to Noah and his sons, could have had none or much, much less mutations than we have today? How do we know how many mutations per generation people had 100 or 200 years ago?
ID proponents (except me and a few others) suggest there is information increase when entropy is reduced. Granville Sewell and others have yet to demonstrate that. I’ve shown, with the example of an ice cube and dead mouse, that more entropy is needed for more (proscriptive) information!
ID proponents (except me and a few others) don’t give simple straightfoward calculations about their claims. I showed a trivial entropy calculation that would be expected of sophomores in chemistry, mechanical engineering, and physics. I’ve not gotten anything comparable from ID proponents comparing a frozen dead rat to a living human. I find that very problematic for using the 2nd law for ID. I’ve argued instead to use violations of the law of large numbers to make ID arguments.
You can see for yourself we crushed a famous evolutionary biologist (named Nick Matzke) with this approach: