Sunday, 19 June 2011

Age estimate for chromosome divergence

JS Allen mentioned a couple blog posts concerning the time the Y chromosome may have gone thru a bottleneck.
The second refers to the article A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa.

Dienekes first post suggests that the divergence of the Y chromosome was 40,000 years ago, the second mentions recent data pushing the date back to 140,000 years. This material is something that Dienekes follows, whereas I am only moderately familiar with it. The journal article covers material on genetic anthropology and my reading on genetics is focused more on disease, but I wish to identify a few assumptions that mean I do not agree with the dates suggested.

My post was on the variation of autosomes, sex chromosomes and mitochondria based on a bottleneck of 3 brothers and their wives. The issue of dating a bottleneck, while related, is a different question. The later requires knowledge of
  1. the variation currently and the likely original sequences; and
  2. molecular clock rates.
Both have significant assumptions and I differ from the authors in several of them.

The article mentions that they attempted independence with regard to 1 then they discuss assumptions relating to using chimp Y chromosomes and human X chromosomes
We obtained a strict-consensus MP [maximum parsimony] tree, which was rooted with respect to either orthologous chimp MSY [male-specific region of the human Y chromosome] sequence... or paralogous human X chromosome sequence...
This hardly seems independent. I reject the use of other species sequences as having relevance, and I do not know whether my assumption of 8 X's to 1 Y at the bottleneck affects the second. So the resulting phylogeny is not necessarily correct.

The problem with molecular clocks is they are not independent either. Dienekes mentions a calibration of 70,000 years for a split but what is this based on? More to the point, in his 2010 post he raises the problem with molecular clocks.
Age estimates vary overall between 6,530 years and 535,755! It is obvious that fast/medium mutating markers provide unbelievably small age estimates (most of them are less than 20 thousand years). However, if we limit the analysis to slow mutating markers, most age estimates are in excess of 300,000 years!

In short, you can arrive at any age estimate you want, by choosing a particular mix of slow and fast mutating markers.
He says (correctly) that we mustn't average different clocks. He rejects throwing them in the trash and argues for identifying the correct clock.
But that is equivalent to having a number of different clocks, some of which tell you that 3 seconds have transpired, and some which tell you that it's been a whole minute. The rational thing to do is not to take an average, but to throw the clocks in the garbage, or figure out what's wrong with them.
I agree, but we are likely to differ on what we consider reliable. I suspect mutation is more rapid than accepted by evolutionists, if so then the clocks are going faster than anticipated. I would like to see some data obtained with fixed dates and generation numbers.

These are just 2 problems with the interpretation. There is also the interbreeding question, the targeted DNA changes versus random mutation, the incompleteness of the data (both complete Y DNA and adequate sampling of the populations). Further data will be interesting.

The greater issue is that (hidden) assumptions markedly affect interpretation. While  interpretations such as given in the paper will be seen as evidence for the evolutionary scheme, so much of the evolutionary paradigm is assumed that it becomes very circular. This is not intrinsically bad, but lack of awareness of assumptions can have the effect that you think your interpretation is stronger than it really is. This can be a potential issue for creationists also, though given their strong focus on identifying underlying assumptions, and that they are working within a paradigm they generally disagree with, I think they are often more attuned to this issue.

5 comments:

  1. As you know, I'm not a Young Earth Creationist. And I think that a scripturally-based presupposition about the earth's age is incompatible with doing good science. But my point in sharing the links was to highlight exactly the sections you quoted in your post -- there are a lot of assumptions that go into these estimates, and the Y-Chromosome Adam may be a lot more recent than we currently think. I think we need to keep an open mind, even if it would lend some credibility to YEC (even though I think they would still be wrong, even if it was 6,000 years for Y-chromosome Adam :-))

    One that's really fascinating to me lately is the ongoing archaeology work at Gobekli Tepe.

    ReplyDelete
  2. Yes, I am aware of your ideas about the legitimacy of various presuppositions and the extent of their scope.

    How credible would YEC predictions need to be for you to reconsider whether your philosophical scepticism about biblical axioms affecting the philosophy of science is well placed? :)

    ReplyDelete
  3. That's a very perceptive question.

    The quick naturalist answer would probably be that it wouldn't matter how accurate the predictions are, and that we shouldn't count ancient records as evidence, regardless.

    However, I doubt that many naturalists would act that way in practice. If naturalism started strongly confirming many of the literalist claims of the Bible, the naturalist would have to conclude that maybe the Bible was intended to be a book about natural science, and that the ancients who wrote it did know a lot about natural science.

    ReplyDelete
  4. The quick naturalist answer would probably be that it wouldn't matter how accurate the predictions are, and that we shouldn't count ancient records as evidence, regardless.

    Something tells me that this won't extend to the non-Judao-Christian records...

    ReplyDelete
  5. @MikeT - I don't think naturalists are in any danger of exhibiting a double standard on this matter. For example, astronomers and cosmologists today do not consider Ptolemy's records, or Greek Myths, to be useful evidence.

    ReplyDelete

Labels

abortion (8) absurdity (1) abuse (1) accountability (2) accusation (1) adultery (1) advice (1) afterlife (6) aid (3) alcohol (1) alphabet (1) analogy (5) analysis (1) anatomy (1) angels (1) animals (10) apologetics (41) apostasy (4) archaeology (22) architecture (1) Ark (1) Assyriology (11) astronomy (5) atheism (14) audio (1) authority (4) authorship (10) aviation (1) Babel (1) beauty (1) behaviour (4) bias (6) Bible (38) biography (4) biology (5) bitterness (1) blasphemy (2) blogging (12) blood (2) books (2) brain (1) browser (1) bureaucracy (3) business (5) calendar (5) cannibalism (2) capitalism (3) carnivory (2) cartography (1) censorship (1) census (2) character (2) charities (1) children (14) Christmas (4) Christology (8) chronology (46) church (4) civility (2) clarity (5) Classics (2) climate change (39) coercion (1) community (2) conscience (1) contentment (1) context (2) conversion (3) copyright (5) covenant (1) coveting (1) creation (1) creationism (36) criminals (8) critique (2) crucifixion (12) Crusades (1) culture (4) currency (1) death (5) debate (2) deception (2) definition (15) deluge (9) demons (3) depravity (6) design (9) determinism (24) discernment (4) disciple (1) discipline (2) discrepancies (2) divinity (1) divorce (1) doctrine (4) duty (3) Easter (7) ecology (3) economics (28) education (10) efficiency (2) Egyptology (9) elect (2) emotion (2) enemy (1) energy (6) environment (4) epistles (2) eschatology (6) ethics (36) ethnicity (5) Eucharist (1) eulogy (1) evangelism (2) evil (8) evolution (13) examination (1) exegesis (21) Exodus (1) faith (22) faithfulness (1) fame (1) family (4) fatherhood (2) feminism (1) food (3) foreknowledge (4) forgiveness (4) formatting (2) fraud (1) freewill (29) fruitfulness (1) gematria (4) gender (5) genealogy (10) genetics (5) geography (3) geology (2) globalism (2) glory (6) goodness (3) gospel (3) government (18) grace (9) gratitude (2) Greek (4) happiness (2) healing (1) health (7) heaven (1) Hebrew (4) hell (2) hermeneutics (4) history (21) hoax (5) holiday (5) holiness (4) Holy Spirit (3) honour (1) housing (1) humour (34) hypocrisy (1) ice-age (2) idolatry (4) ignorance (1) image (1) inbox (2) inerrancy (16) information (10) infrastructure (2) insight (2) inspiration (1) integrity (1) intelligence (3) interests (1) internet (3) interpretation (74) interview (1) Islam (4) judgment (19) justice (23) karma (1) kingdom of God (12) knowledge (15) language (3) lapsology (6) law (17) leadership (2) libertarianism (12) life (2) linguistics (13) literacy (2) literature (17) logic (27) love (3) lyrics (9) manuscripts (11) marriage (17) martyrdom (2) mathematics (10) matter (4) measurement (1) media (2) medicine (10) memes (1) mercy (3) Messiah (5) miracles (4) mission (1) monotheism (2) moon (1) murder (5) nativity (7) natural disaster (1) naval (1) numeracy (1) oceanography (1) offence (1) orthodoxy (3) orthopraxy (4) paganism (2) palaeontology (4) paleography (1) parable (1) parenting (2) Passover (1) patience (1) peer review (1) peeves (1) perfectionism (2) persecution (2) perseverance (1) pharaohs (5) philanthropy (1) philosophy (32) photography (2) physics (18) physiology (1) plants (3) poetry (2) poison (1) policing (1) politics (30) poverty (9) prayer (2) pride (2) priest (3) priesthood (2) prison (2) privacy (1) productivity (2) progress (1) property (1) prophecy (6) proverb (1) providence (1) quiz (8) quotes (419) rebellion (1) redemption (1) reformation (1) religion (2) repentance (1) requests (1) research (1) resentment (1) resurrection (4) revelation (1) review (4) revival (1) revolution (1) rewards (2) rhetoric (2) sacrifice (4) salt (1) salvation (26) science (43) sermon (1) sexuality (16) sin (15) sincerity (1) slander (1) slavery (5) socialism (4) sodomy (1) software (4) solar (1) song (2) sovereignty (15) space (1) sport (1) standards (6) statistics (13) stewardship (5) sublime (1) submission (5) subsistence (1) suffering (5) sun (1) survey (1) symbolism (1) tax (3) technology (12) temple (1) testimony (5) theft (2) trade (3) traffic (1) tragedy (1) translation (15) transport (1) Trinity (2) truth (25) typing (1) typography (1) vegetarianism (2) vice (1) video (10) warfare (7) water (2) wealth (9) weird (6) willpower (4) wisdom (4) work (10) worldview (3)