Thursday, November 29, 2018

I don't get it

Every week or so there are a flood of linked hits to Stones&Bones from porno sites.

I fail to see the connection. Any ideas in the multiverse?

Sunday, November 04, 2018

Archaic foolin' around

I'll be writing a revision eventually. Some really neat new work has been published:

Prüfer, K., Posth, C., Yu, H. et al. A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. Nat Ecol Evol 5, 820–825 (2021).
"... we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common."

"How Neanderthals lost their Y chromosome"
By Ann Gibbons Science Sep. 24, 2020 , 2:00 PM

"The evolutionary history of Neanderthal and Denisovan Y chromosomes"
By Martin Petr, et al
Science, 25 Sep 2020 : 1653-1656

Ragsdale, A.P., Weaver, T.D., Atkinson, E.G. et al. A weakly structured stem for human origins in Africa. Nature 617, 755–763 (2023).

Skov, L., Peyrégne, S., Popli, D., Iasi, L.N., Devièse, T., Slon, V., Zavala, E.I., Hajdinjak, M., Sümer, A.P., Grote, S. and Bossoms Mesa, A., 2022. Genetic insights into the social organization of Neanderthals. Nature, 610(7932), pp.519-525.
Hajdinjak, M., Mafessoni, F., Skov, L., Vernot, B., Hübner, A., Fu, Q., Essel, E., Nagel, S., Nickel, B., Richter, J. and Moldovan, O.T., 2021. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature, 592(7853), pp.253-257.

And I missed this one;

Posth, C., Wißing, C., Kitagawa, K. et al. Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals. Nat Commun 8, 16046 (2017).

DNA sequencing studies starting in 2010 showed that there was interbreeding between H. sapiens, and Neanderthals (1). We also know that there was a third archaic human population known as the Denisovan, named from the Siberian cave where the first examples were recovered (2). They also interbred with modern H. sapiens, and at least occasionally with Neanderthals (3, 4). Finally, it has been shown that Neanderthals had a high amount of inbreeding, and more limited social and economic networks (4).

Modern humans all have H. sapiens mitochondria. Mitochondria are the cell organelles that make the “energy molecule” ATP. They also have their own DNA. So, for openers we know that no offspring from a Neanderthal female and a H. sapiens male mating later reproduced. It is even suggested that the female H. sapiens would be incapable of carrying a Neanderthal sired male fetus to term (5, 6).

Next, there are different descent patterns for the sex chromosomes labeled X, and Y. All females in our genus would have had 2 matched X chromosomes. Their eggs will always (in healthy examples) have an X chromosome. The males have one set of X, and one set of Y DNA. Sperm will carry (in healthy examples) one or the other.

So what does this say about the interbreeding behaviors of these 3 distinct human populations. First, the archaic humans were in decline even at the start of the modern human expansion out of Africa and into Eurasia. A massive glaciation event between 200, and 100 thousand years ago pushed the archaics into a terminal decline. And, as the moderns expanded, the archaic populations declined even faster.

(From Prüfer, 2014)

What we know is that no modern male successfully bred with a Neanderthal female. No female Neanderthal carried a fertile offspring from a modern male. We know that no modern female carried a successful male offspring sired by a Neanderthal male.

For those observed data to make a fairly easy social story, isolated Neanderthal males were adopted out of failing groups into modern human Hunter and Gatherer groups. They mated the modern females, and had a limited number of successful fertile female offspring. If the modern human female was adopted, or what have you, her carrying any Neanderthal genes would have been lost.

1) Green RE, et al. A draft sequence of the Neandertal genome. Science. 2010;328:710–722.
2) Meyer M, et al. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012;338:222
3) Reich D, et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. American journal of human genetics. 2011; 89:516–528.
4) Kay Prüfer, et al. The complete genome sequence of a Neandertal from the Altai Mountains. Nature. 2014 Jan 2; 505(7481): 43–49.
5) Ann Gibbons Modern human females and male Neandertals had trouble making babies. Here’s why Apr. 7, 2016.
6) Fernando L. Mendez, G. David Poznik, Sergi Castellano, Carlos D. Bustamante. The Divergence of Neandertal and Modern Human Y Chromosomes. American Journal of Human Genetics. April 07, 2016 Volume 98, ISSUE 4, P728-734,

Thursday, June 21, 2018

Creato Crap on the Right. On the far-right.

I got clued to a jack-ass, F. LaGard Smith*, who was published by the Daily Caller. The Daily Caller is part of the alt-right, or full-on Neo-Reich. What follows is the creatocrap, with my relies posted to the DB website DISQUS feature. I made a few corrections in this version. The DISQUS thread had the typical creationist twaddle, with the extra special stupid of Joe “Joke” Gallien posting under the name “joe moricone.” “Maricon” is Mexican slang for male homosexual. Joe “moricone” makes enough buttsex, and blowjob comments to earn the title.

JUST SO: The Microbe-To-Man Evolution Story Is Dumb, Bad Science. Why Do Our Kids Learn It As Fact?
9:36 PM 06/15/2018
F. LaGard Smith | Former law professor and the compiler and narrator of 'The Daily Bible'

Dare suggest that America’s school children should be alerted to scientific problems with microbe-to-man evolution, and you can safely predict an outcry from evolutionists along two fronts. First, they protest, there must surely be a hidden agenda to teach the biblical creation story (including Adam and Eve), or the suspected subterfuge of “creation science” or the (even sneakier) argument from intelligent design. Then comes the usual party-line: “You can’t challenge evolution in the classroom, because that would violate the separation of church and state!”

1) the so-called "problems" are not specified. No valid problems are ever specified, Some fake problems are mentioned later that count on the ignorance and bias of readers.

2) The "hidden agenda" of creationists to force a particular, and peculiar religious faith into public schools is obvious. It is not hidden.

3) Adam and Eve creationism is just one little variation of the many creationist dogmas. When the sectarian twits like LaGard Smith spout, they mean their peculiar dogma. His is obviously a variation of some Christian sect. But there are all sorts of religious objections to reality. For examples;

Spetner, Lee 1997 "Not By Chance: Shattering the Modern Theory of Evolution" New York: The Judaica Press

Harun Yahya (Adnan Okbar) 2007 "Atlas Of Creation" Istanbul: Global Publishing

Michael A Cremo, Richard L. Thompson 1998 "Forbidden Archeology: The Hidden History of the Human Race" Bhaktivedanta Book Publishing

Neo-pagan/Native American
Deloria, Vine Jr. 1997 “Red Earth, White Lies” Golden Colorado: Fulcrum

So, teach pagan, Hindu, Muslim, and Jewish creationisms as "proof" of their religions. And then toss Christian creationists on the pile.

Why the religious should fear adding creationist twaddle to the curriculum is that scientists can dismiss creationism as the fraud(s) it is.

Why the knee-jerk outcry against nefarious creationism even if none of the above scenarios are being proposed? Why is the vociferous protest invariably framed in terms of religion rather than science? Simple logic. Even Darwin knew that his naturalistic theory had but one real alternative: the realm of the miraculous, which is to say divine creation. Which, if taught in the classroom would—God forbid—breach Thomas Jefferson’s famous (if not strictly constitutional) “wall of separation.”
The second paragraph of this creationist screed had only on sentence of substance. It was, "Even Darwin knew that his naturalistic theory had but one real alternative: the realm of the miraculous, which is to say divine creation."

So, at least we have a hint of honesty. The only alternative to science is magic. But this claim is also rejected by the religious. For example here are books by clergy who are also competent scientists who don't adopt the false creationist doctrines promoted by cretins like the Institute for Creation Research, Answers in Genesis, or the Creation Research Society.

Ayala, Francisco 2007 arwin’s Gift: To Science and Religion" (Washington DC: Joseph Henry Press- National Academies Press)

Collins, Francis S. 2006 "The Language of God: A Scientist Presents Evidence for Belief" New York Free Press- Simon and Schuster

Carol, Hill, Gregg Davidson, Wayne Ranney, Tim Helble 2016 "The Grand Canyon, Monument to an Ancient Earth: Can Noah's Flood Explain the Grand Canyon?" Kregel Publications

Hyers, Conrad 1984 “The Meaning of Creation: Genesis and Modern Science” Atlanta: John Knox Press

Miller, Keith B. (editor) 2003 “Perspectives on an Evolving Creation” Grand Rapids: Eerdmans Publishing

Ken Miller 1999 "Finding Darwin's God" New York: HarperCollins

Roberts, Michael 2008 "Evangelicals and Science" Greenwood Press

Young, Davis A., Ralf F. Stearley 2008 "The Bible, Rocks and Time: Geological Evidence for the Age of the Earth" Downers Grove: InterVarsity Press

Now recall those are all religious scientists. Many are clergy.

There are pro-science religious. I recommend;

Frye, Roland Mushat (editor) 1983 "Is God a Creationist?: The Religious
Case Against Creation-Science" New York: Charles Scribner's Sons, Inc.

Slifkin, Rabbi Natan
2006/2008 “The Challenge of Creation: Judaism’s Encounter with Science, Cosmology and
Evolution” New York: Zoo Torah and Yashar Books

But do evolutionists who insist that religion’s creation story is the only alternative to evolution’s own creation story not realize the peril of that position? What if those challenging Darwin’s grand theory turned out to be (Holy Scopes!) not Bible-thumpers, but scientists?

As it happens, there’s already a hush-hush open secret among scientists: the quietly acknowledged “Queen of evolutionary problems” — the origin of sex — which, after countless studies, stubbornly defies evolutionary explanation.

We need to smush two tiny paragraphs by LaGard Smith to get anything to refute.

So what of substance?

Some people with desperate need to believe in magic have Ph.D.s in science. There is even a book full,

Ashton, John F. 2001 "in six days: why fifty scientists choose to believe in creation"  Green Forest AR: Master Books

If you read the book you will learn that these creationists were creationists before they studied any science. And most chose to collect science degrees merely as a way to attack science.

And the next false claim by LaGard Smith  is that there is a, “Queen of evolutionary problems” — the origin of sex."


If "sex" evolved then there ought to be physical intermediates either as fossils, living species, or genetic relics.

Well, too bad for Mr. Smith, but we are all good on the evolution of sex.

I'll start with the most basic surviving example of the most primitive sexual critter. It is the modest slime mold. It reproduces by both Mitosis, and Meiosis.

Those primitive cells preserve the some of the biochemistry of your testes, or ovaries.

I find it amusing to mention the sexual apparatus of the most primitive sexual fossil, an extinct ostracod. The males had a penis nearly as large as the rest of their body;

So maybe they were over-equipped.

And then there are the functioning hermaphrodites. Most mollusks, and especially snails are functioning hermaphrodites with simultaneously functioning sexual organs. But they are not alone. One of my favorite fish to catch is a cyclic hermaphrodite. When there is a large dominant male, the females flock. If there are none then a female becomes a dominant male. The species is Semicossyphus pulcher. 

Finally we  must mention the true virgin births of the parthenogenetic whiptail lizards. They "don' need no sex. They don' got no' need for stinking males..." (Apologies to  "Treasure  of the Sierra Madre" fans).

Why is evolutionary sex so threatening that it dare not even be mentioned in textbooks or science classes?

So on to the next bit of creato-trash;

"Why is evolutionary sex so threatening that it dare not even be mentioned in textbooks or science classes?"

Try harder LaGard. I have a copy of the best selling High School Biology text in the United States by Ken Miller, and Joe Levine published by Prentice Hall.

They have pages and pages on reproduction from fungi to humans.

Because of freaky creatoids they play down a bit. Their books sells even in the Bible Belt.

Yes, Ken Miller is the same man who wrote;

Ken Miller 1999 "Finding Darwin's God" New York: HarperCollins
and, 2008 “Only a Theory” New York: Viking Press

And then there is my old copy of Neil Campell's first year college biology textbook, "Biology." There are pages on the evolution of 'naughty bits' in nearly every section. After all, as one of my old professors remarked, "Biology is the 4 F's, "Feeding, Fighting, Fleeing, and Fucking."

Maybe you can fool the far-right, but you cannot fool an educated man.

Given the unique nature of gendered, sexual meiosis compared with non-gendered, asexual mitosis, the first-ever generation of sexual reproduction would have required 1) a never-before-seen male organism and a novel female organism, 2) magically having compatible chromosomes, and 3) a death-defying process of precisely halving their chromosomes, mixing them together in a revolutionary way, and then recombining to produce, not a clone (as in asexual replication), but a unique offspring unlike any on the planet. Not to mention the minor details of geographic proximity and an evolved instinct to mate—all absolutely required in round one of sex to get the sexual ball rolling.

We did a lot of this silly sex denial already. The tight biochemical analysis of evolutionary sex can be found by first understanding that asexual reproduction is not cost free. See as an introduction to real science;
Uyenoyama, M.K., 1986. "Inbreeding and the cost of meiosis: the evolution
of selfing in populations practicing biparental inbreeding" Evolution, 40(2), pp.388-404.

And the famous book;

Margulis, L., 1981. "Symbiosis in cell evolution: Life and its environment on the early earth"

You might try to catch up with the smart kids.

Staley, J.T., 2017 "Domain Cell Theory supports the independent evolution of the Eukarya, Bacteria and Archaea and the Nuclear Compartment Commonality hypothesis" Open biology, 7(6), p.170041.

But I doubt it is in your path.

That’s only for starters. What school children must also never know is that the familiar “tree of evolution” (illustrating evolution’s bedrock assumption of common descent) could never have happened in actual fact. Natural selection could not possibly have provided simultaneous, on-time delivery of the first compatible male/female pair of each of millions of sexually-unique species. (Merely consider the weird, cannibalistic sex of the praying mantis! Or, even more problematic, the first-ever male and female reptiles, mating and reproducing as no amphibians before them.)

So there is a major load of lies, (or just really stupid) in this paragraph.

First, that the “tree of evolution” (illustrating evolution’s bedrock assumption of common descent) could never have happened in actual fact.”

The fact is that the branching pattern of species relationships was known before Darwin. Darwin’s life work was to try to explain what was already known in the 1700s.  LaGard’s next lie is that there is any barrier to sexual reproduction. Every single step in biological evolution is still preserved either in survivors, or in our genes.  LaGard goes into the crazy land with the assertion that there were, “… the first-ever male and female reptiles, mating and reproducing as no amphibians before them.” That is either dishonest, or insane. To the best of my knowledge, and a solid literature search, amphibians are mostly sexual. There are some asexual amphibians. There are more asexual reptiles than amphibians. Oddly, the genetics of the reptiles are more permissive than others. They occasionally allow all female populations to persist.

His biggest lie is that we want to hide this “fact” from school children. It is frauds like him that want to lie to children. 

In his best-selling book, Why Evolution is True, even skeptic Jerry Coyne keenly appreciates where the crux of the evolution debate lies. “A better title for The Origin of Species,” says Coyne, “would have been The Origin of Adaptations. While Darwin did figure out how and why a single species changes over time (largely by natural selection), he never explained how one species splits in two.” (Would it breach “the wall of separation” to share an evolutionist’s corrective with school children?)

Coyne’s own attempt to hypothesize how species might have “split” has to do with “geographic isolation” causing genetic diversions. Problem is, there simply aren’t enough isolating mountains, rivers, or lakes on the planet to explain the origin of tens of millions of different species. So, we’re back to hard scientific reality. If there’s no evolved first generation of any given species, then there could be no evolution into any other species, nor certainly any higher species, most especially us humans.

LaGard closes with a misreading of Jerry Coyne. It is easy to misread Jerry Coyne.

The particular problem is that the “cladistics” fanboys insist they are smarter then Darwin, and have destroyed the old (dead) man’s taxonomic approach.

Worse is that LaGard totally missed is that there is not merely abundant geological diversity to create new species, but that species in a sense collaborate in their mutual evolution. Even Darwin recognized this dedicating two books to various aspects of the problem. These were, 1874 “The Descent of Man and Selection in Relation to Sex,” and 1862 "The Fertilisation of Orchids."

What I find amusing is that Richard Lewontin comes around eventually, and didn't know he was meeting Darwin (again).

Forget religion. Forget the Bible. Forget teaching creationism. On its own terms, the romanticized, politicized, (increasingly even theologized!) microbe-to-man evolution story presented as undeniable fact in the schoolroom is simply bad science. Why should anyone insist that students be taught bad science?

You say not even serious problems with evolution ought to be objectively presented in the classroom? I understand the danger. Do that, and bright young minds might well conclude that the sacrosanct evolution story is not science at all, merely science fiction. Then what creation story will they believe?

* From the Daily Caller, “LaGard Smith is a former law professor (principally at Pepperdine University) and scholar in residence for Christian Studies (Lipscomb University). He is the compiler and narrator of The Daily Bible and is the author of over 30 books. His most recent book is “Darwin’s Secret Sex Problem: Exposing Evolution’s Fatal Flaw—The Origin of Sex.”

Tuesday, June 12, 2018

More "Darwin was a Racist" Bull

14 June, 2018

Matthew Sears a professor of Classics and Ancient History at the University of New Brunswick published a short essay;"Anomaly and Academia: is the Left Really Afraid of Honest Inquiry?"

Sears was critical of a right-wing whine by Anomaly about mean students at a public university angry that Anomaly is opposed to public education.

What I first look at in any publication is the references. It is a habit I developed as a student. In this case, I noticed that according to Matthew Sears, the target of his criticisms, 'Jonny' Anomaly, had promoted a version of Darwinian racism. What Sears wrote that caught my eye was, "Anomaly expands on this line in inquiry in a 2018 article entitled “Defending Eugenics.” Beginning with Darwin himself, Anomaly says, “Darwin argued that social welfare programs for the poor and sick are a natural expression of our sympathy, but also a danger to future populations if they encourage people with serious congenital diseases and heritable traits like low levels of impulse control, intelligence, or empathy to reproduce at higher rates than other people in the population.”

Anomaly claims early on in that essay that "In defending eugenics, I want to reclaim the spirit of authors like Francis Galton and Charles Darwin ..."

I of course smelled a rat because Charles Darwin was dismissive of Galton's Eugenics Society. And, I have read Darwin's core books. I already knew that that Darwin did not propose that social welfare programs were a "danger to future populations." Also as I have written, Darwin was not a racist.

Anomaly in his cited paper pretended to quote from the 1882 printing of the 2nd edition of Darwin's "The descent of Man..." citing page 138. He presented the quote as, "Darwin feared that in developed nations “the reckless, degraded, and often vicious members of society, tend to increase at a quicker rate than the provident and generally virtuous members” (Darwin 1882, p. 138)."

Since I am long familiar with creationists who for years lied about what Darwin supposedly wrote, I have developed the habit of reading the context of any "so-called quote." Here it is in fact;

"A most important obstacle in civilised countries to an increase in the number of men of a superior class has been strongly insisted on by Mr. Greg and Mr. Galton,(19) namely, the fact that the very poor and reckless, who are often degraded by vice, almost invariably marry early, whilst the careful and frugal, who are generally otherwise virtuous, marry late in life, so that they may be able to support themselves and their children in comfort." Darwin expanded on this making the reference explicit by writing on the same page, "Or as Mr. Greg puts the case: "The careless, squalid, unaspiring Irishman multiplies like rabbits: the frugal, foreseeing, self-respecting, ambitious Scot, stern in his morality, spiritual in his faith, sagacious and disciplined in his intelligence, passes his best years in struggle and in celibacy, marries late, and leaves few behind him."

So the opinion that Anomaly attributed to Darwin's was in fact that of Galton, and Greg.

(The Galton book also in Darwin's footnote 19 was citation to "Hereditary Genius' 1870," and will be skipped over for now). The remainder of the quote was a paraphrase of William R. Greg, “On the failure of ‘Natural Selection’ in the case of Man,” Fraser’s Magazine, Sept. 1868, p. 353-362. My former colleague, John Wilkins has made a copy of Greg's 1868 article available on-line. We see that the often timid Mr. Darwin was even then trying to moderate the actual statement by Greg. Here is the actual piece from Frasier's Magazine;

"The careless, squalid, unaspiring Irishman, fed on potatoes, living in a pig-stye, doting on a superstition, multiplies like rabbits or ephemera: the frugal, foreseeing, self-respecting, ambitious Scot, stern in his morality, spiritual in his faith, sagacious and disciplined in his intelligence, passes his best years in struggle and in celibacy, marries late, and leaves few behind him."

It goes on, but you get the gist.

In fact, Darwin spends the rest of the Chapter V (7 pages) dismissing the false claims of Greg in particular. Recall that Darwin's actual opinion of the Eugenics Society proposed by Galton was dismissive, "I am not, however, so hopeful as you. Your proposed Society would have awfully laborious work, and I doubt whether you could ever get efficient workers. As it is, there is much concealment of insanity and wickedness in families; and there would be more if there was a register. But the greatest difficulty, I think, would be in deciding who deserved to be on the register. How few are above mediocrity in health, strength, morals and intellect; and how difficult to judge on these latter heads." Darwin to Galton, January 4th, 1873. 

So, Jonathan Anomaly is either incompetent, or a liar. 

Matthew Sears is either incompetent, or too lazy to read citations.