STORM

I thought this was certainly worth watching when it wasn't all cool and animated. Now of course it is twice as cool. Well not exactly, but it is fun, and if you missed it the first time I posted it, well here you go, the nine minute beat poem STORM, by Tim Minchin, now cooler than before.

Answers Not In Genesis: Where are the uniform genetic bottlenecks predicted by Noah's Flood?

One problem facing the fundamentalist, biblical creationist is the relative tractability of the predictions the Book of Genesis makes when taken literally. The timescales are relatively short, and the events depicted in Genesis, if taken literally, are dramatic enough that evidence for them would not all be washed away in deep time. These predictions form quite easily falsifiable hypotheses. That is to say they are the very kinds of claims that science is most capable of assessing. Also, the predictions are all fairly obvious. So if there really is a Creation Science where is this relatively easy, publishable research on these problems that are so amenable to the scientific method? That is sort of a trick question, because the predictions of a literal reading of the Book of Genesis have already been falsified by science. Of course you would not know this if you only listened to folks like The Institute for Creation Research, or only hung out at the ridiculously unscientific intellectual pride of Kentucky, the Creation Museum. No creationist organization is really very interested in actually doing science. That may seem like a harsh generalization but I invite you to go to their websites, and read their literature and draw your own conclusions. What is called Creation Science is simply a lot of hand waving and special pleading to exempt a cherished dogma from the rules of evidence. They exist to defend the faith even at the expense of the truth. For the creationist this may be good thing. There is simply no research left for them to do.

In the Beginning....God smote genetic diversity
Taken literally, the book of Genesis makes several very specific predictions about the genetic diversity of all life on earth. Here is one very specific prediction that we can derive from Noah's Flood concerning the genetics of all life on earth.

1. All life on earth passed through a very narrow population bottleneck around 4,500 years ago.

2. All species were dramatically reduced to very few in number.

3. All terrestrial, and some semi-aquatic animal species were reduced to either 2 individuals, or 14 individuals.

4. Therefore all terrestrial/semi-aquatic animal populations should demonstrate a very uniform genetics.

5. Variation in this uniform genetics should be able to be traced back to around
4,500 years ago (within a reasonable margin of error).

6. All animal populations should demonstrate the presence of extremely small
populations at the time of the population bottleneck (at least <50).

7. Organisms not deliberately transported on the Ark also would have experienced
a massive population crash, and would also demonstrate marked genetic uniformity
that could be traced back to 4.500 years ago (within a reasonable margin of
error).

I will explain what a population bottleneck is and what consequences it tends to have on a population in a moment, but first....

A brief aside about DNA, genes, and mutation:
I'm going to be using some shorthand in the following paragraphs, and it may help you, if you aren't steeped in biology to have a refresher of your long forgotten high school biology. Genes are stretches of DNA (deoxyribonucleic acid) that code for some cell product, cytochrome-b say, or some other protein. DNA itself is a long two stranded polymer of nucleic acids composed of adenine, guanine, cytosine, and thymine, (A,G,C and T respectively)that forms the classical double helix (think of a ladder that has been spiraled around itself, still linear, but twisted). The nucleic acids form the rungs of the ladder, and every three letters in a gene (a segment of the DNA that codes for some product) is a specific code for a specific amino acid. So in a gene the triplet thynine adenine cytosine (TAC) codes for the amino acid methionine. Other triplets code for other amino acids. Mutations are errors of DNA replication. These errors alter the code, sometimes subtly and sometimes dramatically. The DNA triplets TAC and TCC do not, for instance, instruct a cell to utilize the same amino acid.

When populations diverge, genetic variation between the populations begins to build if there isn't a great deal of interbreeding between them, so their common genes will reveal differences in their sequences of As Ts Gs and Cs (and the triplets they make). No population will have the exact same sequences for the same gene (indeed there may be many different versions of a gene). For instance, different populations of humans may have significant differences in their genes for the manufacture of the structural protein keratin. To establish a reasonable estimate of when these varieties diverged, we need to know the mutation rate for the gene in question (the rate at which the nucleic acid codes are altered and how often those alterations are uncorrected, plus the generation time for the species in question) we need lots of sequence data from numerous populations, and we need powerful modern computers to perform the rather large analysis/comparison of the sequences and their differences.

I am intentionally leaving out the role of RNA (ribonucleic acids) in this, but I don't think we need to wade too deeply into transcription and translation, and protein synthesis. For our purposes what you need to is some knowledge of what a gene is, how it is altered and how examining those genes and their sequences actually gives scientists quite a window into the history of divergence of the genes (and thus the populations) in question.

Population Bottlenecks
A population bottleneck is simply any event that, more or less randomly, and significantly reduces the size of a population. Any such reduction in population size will also result in a reduction in that population's genetic diversity as well. It is also unlikely that the survivors of any such event will be carrying a representative sample of the genetics of the population as a whole. This is why population bottlenecks are also often referred to as genetic bottlenecks. A significant loss in population size will translate to a significant loss of genetic diversity. On one side of the event any sampling would reveal high numbers of individuals and high genetic diversity (as measured in the diversity, and frequency of alleles for given genes) and on the other side of the bottlenecking event sampling would reveal low numbers and low genetic diversity.

Perhaps the best way to illustrate this would be through a simple example (that I think I am stealing from my old Population and Community Ecology professor, Brent Smith at least in part, lets hear if for Earlham College Biology!).

Say we have a population of 10 lemmings moving up a mountain, or at least a really large hill together, perhaps they are migrating, or emigrating to new land with greener grass. Assume five of those lemmings are male and five are female. In the course of their travels up the hill a large rock comes tumbling down the hill (a mini avalanche caused by hikers pushing boulders down the mountain or hill or whatever) and our large rock crushes all five males who were clumped together for some reason peculiar to male lemmings. We can see with out much effort the kind of disaster this has just had on the population. The population went from possessing five Y chromosomes (any male will have XY sex chromosomes) to possessing no Y chromosomes. It is important to note that a Y chromosome isn't a gene. A chromosome is a specific long strand of DNA, that contains genes. In this example the loss of the Y chromosome represents a significant and dramatic loss of genetic diversity (in this case, all the genes contained on the Y chromosome).

We can see that the random sample that survived isn't representative of the original sample (all our survivors are females bearing only XX chromosomes). It will also be unlikely that each of the females that survived will all be pregnant with each of the dead males, so even if one or two females are pregnant and the population isn't doomed out right, it will still be dealing with very low variation along the Y chromosome, and not just there either. Assume one female was pregnant by one of the males that would give the population one Y chromosome and its alleles (an allele is a variant of a gene). Over time genetic variation would be rebuilt in the population through mutation, possibly horizontal gene transfer (don't worry about it) and the process of genetic recombination that occurs when sex cells (sperm and egg) are made. We probably needn't go further than that.

My hypothetical lemmings (or Brent's hypothetical lemmings)illustrates the way in which population/genetic bottlenecks can influence the size and genetic composition of a population, and we now understand that lost genetic diversity would be rebuilt largely by mutation in populations that manage to survive long past the bottlenecking event (in my freakishly simple example, this could only be done if at least one female was pregnant). One more thing to note is that the occurrence of a bottlenecking event would be identifiable to anyone studying our lemmings. Researchers would note a rather homogeneous genetics characterized by very little variation in genes on the Y chromosome certainly and for many other genes as well. It would be possible for our hypothetical researchers, if they knew the mutation rate for certain genes (the rate at which the strand of DNA in the gene is altered), to calculate an estimate of how long ago different versions of our hypothetical lemming genes (alleles) diverged by comparing target genes across the population. That is they could examine and compare the variation in target genes, typically highly conserved genes (which is a technical way of saying genes that change slowly over time due to crucial functioning of their products). A conserved gene is simply a gene that isn't free to alter too much or too rapidly because alterations in its code tend to have have negative effects on the functionality of that gene's products, which translates to negative effects on the organism bearing such mutations.

With that ground covered we are in a better position to ask whether or not science has found evidence of population/genetic bottlenecks, and if so we can ask whether or not the bottlenecks conform to the predictions of Genesis (that all, or almost all, extant organisms will demonstrate a significant bottleneck with a point of origin around 4,500 years ago).

The answer to the first question is yes. There is no shortage of genetic bottlenecks to be found in nature. However they do not indicate any kind of uniform point of origin. Cheetahs for instance passed through a bottle neck around 10,000 years ago, which is around the tail end of the last ice-age (Menotti-Raymond and O'Brian 1993). Though there is some disagreement over the exact time frame, the range of times given isn't supportive of the 4,500 year hypothesis at all.

Humans seem to have passed through a least one severe population bottleneck, perhaps more. While the matter is by no means settled it seems safe to say that the low genetic diversity among humans does little to support any fundamentalist reading of the Genesis story. The whole genesis account is of course further damaged by the fact that whatever the form of the bottleneck humans faced (Toba disater around 70,000 years ago, or long bottleneck, or some odd combination of smaller bottlenecks, we are left with the well documented human population growth at around 50,000 years ago (Ambrose, 1998). There is no sharp and precipitous population crash from which to recover after that, which is predicted by creationists.

Humans and cheetahs are hardly the only species to demonstrate such population bottlenecks, here is a short list with estimates for the time of their respective bottlenecking events:
Albatross (Amsterdam and Wandering)- >840,000 years ago
Northern Elephant Seal- ~121 years ago
Giant Panda- 43,000 years ago
Golden Hamster- 81 years ago
Orangutan- ~170,000 years ago

We needn't go further really. What we can see from these examples is that the Genesis hypothesis fails pretty miserably in its prediction of large scale genetic uniformity across all phyla, originating fairly recently, and within recorded history. I have never seen this rather obvious prediction discussed among creationist authors. I suspect that curious state of affairs stems largely from the fact that creationists tend not to be biologists but theologists, or engineers if they have any science background at all (not entirely of course). A real science minded creationist would certainly see the merit of what I am suggesting here. Where is this research? It will not be forthcoming. I predict what they will produce when confronted by this will be oodles and oodles of hand waving, and magical, supernatural thinking to sweep away the fact that they have no positive evidence for their hypothesis. I can hear it now:
Well God simply touched up the genetic diversity of many species after the flood.
God gave the organisms only the amount of genetic diversity he, in his loving, merciful wisdom, knew they would need.
Genetic diversity isn't really affected by small population sizes, or events that reduce populations to 2-7 pairs of individuals (Genesis states that Noah took either a single pair of critters, or seven pairs).
It is in evasions like that that intellectual suicide is most easily identified.

A mini-glossary

chromosome A chromosome is a particular long strand of DNA (genetic material, comprised of nucleic acids composed of various genes. Different chromosomes have different genes.

gene A unit of heredity. This is actually defined slightly differently by different groups of biologists. For our purposes we will follow the molecular biologists and say that a gene represents any segment of DNA that, as my Penguin Dictionary of Biology puts it, "codes for cell products." So at its simplest, a gene is simply a strand of DNA that creates something in cells. To say that is a gross oversimplification of the state of affairs is to understate the matter considerably.

allele An allele is a variant of a gene. Variation in a gene is built by mutation, which is to say it is built of random changes in the DNA code that are the instructions for building some product (behavior, structure, protein etc). A good way to think of the matter is as follows. The gene may be formally thought of as a specific region of DNA on a specific chromosome, that "creates" some product. Alleles are the various ways in which that product is coded in different bodies of a given species. Maybe iris color is represented by a specific region of the DNA along some chromosome (the gene) and different bodies in a population will have different forms of that gene, green, hazel, brown, blue (the alleles).

Bibliography
Ambrose, S.H. 1998. Late Pleistocene human population
bottlenecks, volcanic winter, and
differentiation of modern humans. Journal of Human Evolution (1998) 34, 623–651

Arora N, Nater A, van Schaik CP, Willems E, van Noordwijk MA, Goossens B, Morf NV, Bastian M, Knott C, Morrogh-Bernard H, Kuze N, Kanamori T, Pamungkas J, Perwitasari-Farajallah D, Warren K, Verschoor E, Krützen M. 2010. The effects of Pleistocene glaciations and rivers on the population structure of Bornean orangutans (Pongo pygmaeus). Proceedings of the National Academy of Sciences, USA 107, 21376-21381.

http://evolution.berkeley.edu/evosite/evo101/IIID3Bottlenecks.shtml

Dawkins, R. 2004. The Ancestor's Tale: A Pilgrimage to the Dawn of Evolution. Houghton Mifflin Company, New York New York.

Menotti-Raymond, M and O'Brien, S.J. 1993. Dating the genetic bottleneck of the African cheetah. PNAS April 15, 1993 vol. 90 no. 8 3172-3176

Milot, E., Weimerskirch, H., Duchesne, P., Bernatchez, L. 2007. Surviving with low genetic diversity: the case of albatrosses.Proc Biol Sci. 2007 March 22; 274(1611): 779–787

http://en.wikipedia.org/wiki/Population_bottleneck, last modified, 13 June 2011 at 20:17

A long response to Twinkledorp

(I was going to post this in the comment section of the last entry of IDGOFB but blogspot claims I used too many characters. So here is my long response to one of Twinkledorp's posts)

Twinkledorp,
I thought it might be fun to address this as well.

"Just consider me a Skeptic. Whilst you may believe your scinetific methods tell you one thing, I am not going to go on 'faith' and believe evolution is all that you believe it to be."

And what are you going to "go on" to reject the Neo-Darwinian Synthesis? It appears at first that we be both believe that faith is an exceedingly bad thing. Do you really have good grounds to reject the findings of nearly 200 years of biology? If you do I think you should publish them, if you don't (and judging by the reasons you give below, we can see you don't) aren't you really just staking out another contradictory faith claim?

"What others 'know as a scientific fact' is of little importance to me. I have yet to be convinced for a few reasons:"

This could be rephrased to I really don't care what the evidence demonstrates because I have this a priori conclusion from which I will not be budged in the slightest.

"1). Though born Atheist, my free thinking process has lead me to the conclusion God exists, though not the Christian or religious God
that you might assume I may be referring to."

Interesting, but essentially content free. Your "free thinking" is meaningless if it isn't backed by some form of verifiable evidence. You could be absolutely, completely, devastatingly correct in every way, and everyone would be absolutely correct to reject your new paradigm if you cannot adduce anything to back it up but your thought, and your, ahem, logic.

"2).
During darwin's time, Science and Religion were at war. Scientists were scratching at the bit to 'give ot to' the Religious folk and there was no way in Hell they were going to have God play any part in the evolutionary process were thus 'intelligence in design' had to be excluded from their conclusions."

Actually this is precisely the opposite of true. Lyell, the great geologist and good friend of Charles Darwin was a more or less orthodox religious man. He, in fact, seemed to hope that Darwin was wrong despite being a very great admirer of Darwin's work. But Lyell also was one of the first to realize how mind-numbingly old the Earth really was. Alfred Russel Wallace, co-discover of natural selection with Darwin, maintained a belief in God (a god of some kind any way) because he simply couldn't think of a way humans could have evolved. I could go in this way for some time. Darwin was probably the only textbook atheist in the bunch (though he was't always so, and his theory of evolution by natural selection probably had less to do with his loss of faith than did the problems of theodicy).

Also while you may say that scientists were "scratching at the bit" (I think you mean tugging at the bit, or chomping at the bit) to, as you so elegantly say, "give ot to" religionists, this seems largely false. Darwin, at least, waited decades to publish because he was sensitive to the injury it would/might do to people's religious sensiblities.

Most of the scientists of Darwin's time would have been believers who didn't take the scriptures literally, they, like many a scientist before them were curious about the true nuts and bolts of God's creation, not what they considered the metaphors of holy books. What is true is that religion has always had an uneasy relationship with an honest pursuit of the truth because it so easily makes canards of holy canon. So, probably as far back as Hypatia (and I would imagine even further) to now, clerics pitch a fit when cherished dogma is challenged by the rigorous findings of any science.

Also there has, as yet, been no need, nor any evidence that would imply an "intelligence in the design" of things. It all just looks like one example after another of "survival of the stable." Which is a great, if simplistic, descriptor (not my coinage) of the natural world.

Also, this is all incredibly irrelevant. Whatever the case was in Darwin's time has no real effect on the science that took place after. The evidence is what the evidence is, and it was compiled by believers, unbelievers and agnostics, and it all seems to support evolutionary biology.

"This poses a massive credibility problem and therefore any conclusions drawn should be taken with a grain of salt. After all, the main objective at the time (which continues today) was winning the war with Religion therefore objectivity was sacrificed in the name of 'Victory'."

There was no war on religion, as I stated above. Scientists just work on their problems, and often unwittingly step on cultural landmines. Scientists are comprised, as I said above, of believers and unbelievers of every stripe. One of the most comprehensive efforts at public understanding of evolutionary biology, and explaining the evidence that supports it was written by a fairly standard god-bothering Christian. The book (excellent by the way) which you should definitely read is Evolution: What the Fossils Say and Why it Matters by Donald Prothero. Its kind of pricey but it will give you one of the best overviews of the state of evo-bio, probably not offend you, and provide plenty of papers for you to track down and read from its literature cited section.

Sorry Max11.

I doubt this very much. Its Max II not, 11.

Evolutionist will need to do a bit of evolving themselves to ensure objectivity and good old common sense in their work unless of course you believe houses are built without blusprints, and people speak 1st and then think, which in your case I could almost be convinced is true.

Objectivity in the pursuit of scientific discovery arises from transparency of experimental design and the replicablity of results. Not from worrying over much about the kinds of thoughts particular researchers have about the status of the universe. Incorrect findings, errors, fraud will be discovered with time and research.

And common sense is useless in science. It leads more often than it does not to rather severe errors. Our common sense fails when it is put to the task of thinking about deep fundamental aspects of nature, human nature included, because nature is vastly weirder than our day to day lives.

Stop by and visit my site anytime.

Do leave a url and I will.

"Twinkledorp Peabody IV."

Fascinating name.