Monday, May 30, 2011

Another look at Bias and Prayer

I ran across this story today which I hadn't heard about before so I did some investigation and thought I would share my findings because it shows how Confirmation Bias leads to false conclusions.

Back in November 2007 Georgia (the whole southeast) had been experiencing a severe drought for some 18 months. So Georgia Gov. Sonny Perdue announced he would hold a public prayer to ask god for relief from the drought because, as we all know, "The only solution is rain, and the only place we get that is from a higher power," said Perdue spokesman Bert Brantley.

So the first question here (which apparently didn't occur to many in the media), is how many people, how many farmers prayed during that year for rain already over that year?  Keep in mind that those thousands upon thousands of prayers went unanswered.

Now read the very last line of this report about the upcoming event:
Now in Georgia, there is a little rain predicted, but not enough to end a drought.
"There is a little rain predicted," well now, isn't that convenient. Let's schedule a public prayer right around the time SCIENCE is already predicting precipitation. And if it so much as sprinkles on that day? Thank GOD we prayed.  I'm disgusted by this kind of duplicity honestly.  They wait 18 months to make a big deal out of a prayer meeting when meteorologists just happen to be predicting precipitation.  I'm also a little ashamed that people fall prey to such simplistic manipulation.

And then people (see this YouTube video) take ONE instance out of what could be tens of thousands and count that as a rousing success DESPITE the fact that the drought continued to worsen and lingered on through 2008, it got much WORSE in many locations after Nov 2007 and it was relieved only in late 2008 and 2009 for some regions.  This is a perfect example of Confirmation Bias
Drought conditions persisted and actually continued to worsen during December. This was especially true during the first half of the month when unseasonably warm, dry weather prevailed across the region
Lake Lanier in northeast Georgia and the main water supply for the Atlanta metropolitan area, dropped to its lowest level in history on December 28, 2007
Tell ya what, next time there is a drought, wait 6 years before praying and see if it corrects itself without the prayer and only then pray when meteorologists are predicting the weather to be the absolute worst, not when they are finally predicting some rain.

A detailed analysis of the 2006-2008 Drought:

See also:

Monday, May 16, 2011

The Chicken-Egg problem, an evolutionary parable

Caveat: this is only slightly edited text, written very much off-the-cuff.  Please help me correct any errors you spot.


I made a twitter post today which read: "Evolutionary theory does NOT indicate a human male & female pair that is a bottleneck, common ancestor: True or False?"

That was the best I could do in 140 characters but I think I captured the essence of the question. The main purpose of this was to challenge people to think about how such evolutionary processes might work.

To explain in a bit more detail - the question is, for speciation to occur does a M/F pair of the NEW species need to pre-exist or not. If we cannot breach this barrier then evolution would be dead in the water.

I also have found this is an extremely common misconception amongst people who do not understand evolution that there is this requirement for a new species to be 'magically' created in pairs. They don't seem to understand that speciation happens in a population of viable procreation partners.

And while it is possible, in theory, that two individuals could just happen to have the SAME genetic mutation at the same time AND find each other it is simply not necessary for evolutionary speciation to occur (and co-mutation seems unlikely to be the norm).

So, the correct answer is True - evolutionary theory does NOT predict or require that there would be M/F pairs created for speciation to occur. Speciation is really the product of culling the population rather than procreation. That is, the isolated species is created when other 'bridge' members of the population die, rather than when it is born.

Thought Experiment:

If you isolated 2 groups of 100 rabbits (call them A and B) each then wait 200My with each group exposed to different selectivity criteria (e.g., group A in harsher, colder climates and group B in warmer) what would we expect to find? Well, the A' rabbits would all be fairly similar to each other but very different from the A rabbits - they might have smaller ears, warmer fur, cold-adapted respiratory systems, etc. Likewise, the B' rabbits would be similar to each other but again different from the original group B. They might have lost their dense fur for example.

And let's say that you saved some embryo's from the original population and raise them into 'normal' rabbits - these original rabbits might be completely unable to bred with either A' or B' (each generation spent in isolation would slightly increase this chance).

Each group will likely have speciated over that time but at no point would there be a unique M/F PAIR in the diverged lineages. They would ALL be related to each other with finer gradations of genetic variations.

Detailed Example

This next one is very technical but will demonstrate, I hope very clearly, what happens in a population leading up to speciation and why a M/F pair isn't required for the process.

First, please note that this account is FICTIONAL, although it is based on science I'm essentially paraphrasing. For example, there really IS an OCX family of genes which make Ovocalyxin proteins which are involved in egg-shell production (search for OCX-32, OCX-36, OCX-21 if you want to learn more). But I'm calling OCX1 my baseline and just numbering the successive mutations, I'm not using the SAME numbering scientists use.

We will look at three gene families (groups of genes) in a population of Gray junglefowl (the probable ancestor of the domesticated chicken) and we will crack the old chicken and egg problem (please hold your groans until the end).

Gene #1 will be OCX in the Ovocalyxin family of genes and is related to egg-shell production
Gene #2 will be SLIT, an axon guidance molecule in embryonic development (again, a real gene designation - but fictional mutations for purpose of demonstration)
Gene #3 will be MHC major histocompatibility complex - which controls the antigens affecting immune response; there are many possible sources of evolved sexual incompatibility; I'm using an antigen example

In each case, there exists a fairly large, and viable set of variants for these genes. We will number the variants start with 1 as the baseline for our population of Gray junglefowls as {1,1,1} which means OCX1, SLIT1, MHC1 while {1,1,2} has mutation variant MHC2.

In our make-believe world, the Gray junglefowls have softer-shelled eggs which are easily poached (no groans!) by snakes and other small animals, the eggs take 28 days to mature and hatch, and the animals have compatible antigen systems.

Also, imagine in our population there are 1000's of fowl although we will focus on just a few individuals. I will call each fowl F and a number (e.g., F1, F2, F3).

Our story begins when F1{1,1,1} mates with F2{1,1,1} and has offspring F3{1,2,1}. This lucky fowl develops and hatches in only 26 days, giving less time for predation to occur resulting in a slightly increased chance of survival.

F3{1,2,1} grows up and mates with F4{1,1,1} giving several Fn{1,1,1} offspring and two fowl F5{1,2,1} and F6{1,2,1}. The Fn's are eaten before they hatch but F5 & F6 survive due to the shorter 26 day incubation period thanks to the mutation to their SLIT gene complex. Hopefully it is easy to see how this trait could easily spread through the population. Year after Year, SLIGHTLY more of the {1,2,1} variants survive until finally the distribution is 95%{1,2,1} and only 5%{1,1,1}.

Is this minor mutation a new species? Well no, they can all freely interbred and while we think of Gray1 as having a 28 day incubation period and the 26 day incubation period of Gray2 alone doesn't seem like enough to call it a new species. Thanks only to the power of genetic sequencing we can SEE the exact change that occurred between the two groups in the population.

Possibly 100's of more years go by -- other genes mutate, maybe they get bigger or smaller feathers or their colors shift slightly - but still nothing we consider 'major' and still all sexually compatible with each other.

Finally, a single F7{2,2,1} is born and happens to survive. When F7 lays an egg is has a tougher shell than eggs from other Gray's! This harder shell thwarts several of the predators of the softer shells. The {2,2,1} mutation spreads quickly through the population as not only do these fowl survive predation it forces the predators to eat more of the {1,2,1} and {1,1,1} fowl.

The population quickly (in geological time) changes to 95%{2,2,1}, 3%{2,1,1}, 1.5%{1,2,1}, 0.5%{1,1,1} - almost all of the SLIT1 variants are now gone having been eaten before hatching either by taking too long or being easier targets.

There are likely MANY genetic variations which prove unviable, these fowl die before they are born or are unable to reproduce. Time marches forward. It is here where we need to understand that fowls are Diploid genetically (they have two copies) and thus can express dominate or recessive traits. I will mark genes which are different on the chromosome with a prime (e.g., 1'2 means it has both 1 and 2 variants).

Our next shift involves the MHC complex - this is the true beginning of our speciation event. F8{2,2,2'} is born, this minor shift in the MHC complex gives this variant a slightly lower chance of successful sexual reproduction (but possibly an increased resistance to a common disease).

F8{2,2,1'2} can then mate with F7{2,2,1}s giving both types of offspring (those like F8 and those like F7). At first, there would be no mating issue as MOST mates would be compatible, so the variant is not detrimental at this stage and it is over the long haul where genetic variations compete with one another. Even seemingly detrimental variants which do not prohibit reproduction can flourish for a time.

Eventually our fowl friend will meet another like itself and one F8{2,2,1'2} will mate with another giving three possible offspring:

F7{2,2,1} 25%
F8{2,2,1'2} 50% (1'2 and 2'1 are the same)
F9{2,2,2} 25%

And here is where our new variant encounters a slight challenge. F9's cannot mate successfully with F7 or lower (their MHC complexes are too incompatible due to the now dominate MHC2) and only half the time with F8's.

But we can see from the above that F8's are favored to become the most frequent so our fine feathered fowl has a decent chance of making it. And, unlike the mutation event itself, we do NOT have only one shot here. There can fairly quickly be 100's or thousands of F9's trying to mate and their chances are better than it might seem (50% chance with 50% of the population and 100% chance with 25%). And if there is some ancillary benefit to {2,2,2} like disease resistance that could kick it over the top.

Let's even say it has failed 1000 times before but THIS time it makes it. We suddenly have a very robust population of fowl with very diverse genomes but with a peak of 90%{2,2,2} and 8%{2,2,1'2} fowl.

So now you ask, where are the Chickens? These are all just Gray's right? Well, it is a Gray with a hardened shell, faster incubation, and sexual incompatibility with any {1,1,1} population that was perhaps isolated from our earlier group.

Let's say there are further enhancements {3,2,2} and {2,3,2} which result in a higher population of {3,3,2}'s and eventually {4,4,2}'s, {4,4,2'3}s and {4,4,3}s which are even more disease resistant. All these changes using the same processes above.

So now we have a fowl {4,4,3} with an extremely tough & bacteria resistant shell, a 21-day incubation period, and is more robust against diseases. This FIRST {4,4,3} is our first True Chicken. However, it is still sexually compatible, at various levels with the {4,4,2'3} fowl which are not quite True Chickens.

We now require only ONE more piece of information and we can resolve the famous Chicken vs Egg Dilemma. What do you mean by 'egg'?

a) An egg that CONTAINS a True {4,4,3} Chicken - the egg which contained the first True Chicken would have come from two {4,4,2'3}-Almost Chickens -- therefore the Egg would have come first.

b) An egg FROM a True {4,4,3} Chicken - then the True {4,4,3} Chicken must have come first

c) Any type of egg at all - eggs in general are much much older than chickens of all kinds

Supporting Data

If you chart out the allele frequencies over tme you get a graph that looks like this (from Wiki):

Here is a very nice study on allele frequency distribution in geographically diverse populations of mice.

Another study in which e coli, under observed laboratory conditions, evolved the ability to process citrate with very detailed genomics data through the generations.

Learn about the HOX gene complex, which is a major factor in developmental morphology (and some cool examples in Drosophila).

Meet Prdm9 (PR domain-containing 9), the gene responsible for much of the genetic shuffling that is done when sperm eggs develop from germ cells (requires NewScientist account). This gene comes in many variations which alter how much shuffling is done and at which points (and some variations may be involved in certain kinds of genetic diseases) - more on Prdm9. Nature Genetics journal paper: doi:10.1038/ng.658

Learn about Histone and its role in shaping and regulating DNA expression.

A critical step in the fertilization process is Oocyte activation, within this process is the DNA synthesis from the two gametes (called syngamy, this combines the DNA from each gamete) and there are complexes of genes which must interlock or the synthesis will not happen, even if the DNA is otherwise compatible. This is one of the mechanisms of speciation by sexual incompatibility in complex organisms (penis shape and size is another in some species, e.g., ducks). Differences in these genes are involved in some cases of human infertility which could eventually lead to speciation in humans.

Interesting paper on the speciation of Yeast due to reproductive isolation:
Incompatibility of Nuclear and Mitochondrial Genomes Causes Hybrid Sterility between Two Yeast Species.

Saturday, May 7, 2011

Where is the evidence for Evolution?

Certain "types" of people seem to ask "Where is the evidence for Evolution?" persistently, apparently unaware of the hundreds of thousands of scholarly papers on the subject as well as untold numbers of books - which they are either allergic to or incapable of understanding.

What amazes me is that these people are apparently incapable of following the simplest arguments and yet, are simultaneously, smarter than the smartest people on earth who have been educated in this subject - despite not actually knowing a thing about the subject in question.  They cannot even seem to make honest claims about evolution  It's an extraordinary juxtaposition of traits but who am I to question such things. Ignorance truly works in mysterious ways.

So, here is just a TINY sampling of evidences for evolution. If you want to make a good argument that evolution is invalid, ALL you have to do it write a rebuttal on all of these papers, submit your brilliant rebuttals to the relevant, peer-reviewed journals and get it published.


Theobald, D. L.  2010.  A formal test of the theory of universal common ancestry.  Nature 465:219-223

Adl, S., Leander, B.S., Simpson, A.G.B., Archibald, J.M., Anderson, O.R., Bass, D., Bowser, S.S., Brugerolle, G., Farmer, M.A., Karpov, S., Kolisko, M., Lane, C.E., Lodge, D.J., Mann, D.G., Meisterfeld, R., Mendoza, L., Moestrup, Ø., Mozley-Standridge, S.E., Smirnov, A.V., and Spiegel, F. (2007) Diversity, nomenclature, and taxonomy of protists. Syst. Biol., 56, 684-689.
Adl, S.M., Simpson, A.G., Farmer, M.A., Andersen, R.A., Anderson, O.R., Barta, J.R., Bowser, S.S., Brugerolle, G., Fensome, R.A., Fredericq, S., James, T.Y., Karpov, S., Kugrens, P., Krug, J., Lane, C.E., Lewis, L.A., Lodge, J., Lynn, D.H., Mann, D.G., McCourt, R.M., Mendoza, L., Moestrup, O., Mozley-Standridge, S.E., Nerad, T.A., Shearer, C.A., Smirnov, A.V., Spiegel, F.W. and Taylor, M.F. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol., 52, 399-451.
Adoutte, A., G. Balavoine, N. Lartillot, O. Lespinet, B. Prud'homme, and R. de Rosa. 2000. The new animal phylogeny: Reliability and implications. Proceedings of the National Academy of Sciences (USA) 97:4453-4456.
Ahmad, S., A. Selvapandiyan, and R. K. Bhatnagar. 1999. A protein-based phylogenetic tree for Gram-positive bacteria derived from hrcA, a unique heat-shock regulatory gene. International Journal of Systematic Bacteriology 49:1387-1394.
Anderson, C. L. 1998. Phylogenetic relationships of the Myxozoa. Pages 341-350 in Evolutionary Relationships among Protozoa (G.H. Coombs, K. Vickerman, M.A. Sleigh, and A. Warren, eds.) Chapman & Hall, London.
Anderson, C. L., E. U. Canning, and B. Okamura. 1998. A triploblast origin for Myxozoa? Nature 392:346-347.
Andersson, S. G. E., A. Zomorodipour, J. O. Andersson, T. Sicheritz-Ponten, U. C. M. Alsmark, R. M. Podowski, A. K. Naslund, A. S. Eriksson, H. H. Winkler, and C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133-140.
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Wednesday, May 4, 2011

Response: Rabbi Eric H. Yoffie: The Sad, Naive Atheism of Christopher Hitchens

Response to: Rabbi Eric H. Yoffie: The Sad, Naive Atheism of Christopher Hitchens

The biggest problem with Yoffie's claims are passages such as these in his own, supposed, "Holy" books.
Deuteronomy 7
1 When the LORD thy God shall bring thee into the land whither thou goest to possess it, and hath cast out many nations before thee, the Hittites, and the Girgashites, and the Amorites, and the Canaanites, and the Perizzites, and the Hivites, and the Jebusites, seven nations greater and mightier than thou;
2 And when the LORD thy God shall deliver them before thee; thou shalt smite them, and utterly destroy them; thou shalt make no covenant with them, nor shew mercy unto them
Deuteronomy 13
6 If thy brother, the son of thy mother, or thy son, or thy daughter, or the wife of thy bosom, or thy friend, which is as thine own soul, entice thee secretly, saying, Let us go and serve other gods, which thou hast not known, thou, nor thy fathers;
7 Namely, of the gods of the people which are round about you, nigh unto thee, or far off from thee, from the one end of the earth even unto the other end of the earth;
8 Thou shalt not consent unto him, nor hearken unto him; neither shall thine eye pity him, neither shalt thou spare, neither shalt thou conceal him:
9 But thou shalt surely kill him; thine hand shall be first upon him to put him to death, and afterwards the hand of all the people.
10 And thou shalt stone him with stones, that he die; because he hath sought to thrust thee away from the LORD thy God, which brought thee out of the land of Egypt, from the house of bondage.
14 Then shalt thou enquire, and make search, and ask diligently; and, behold, if it be truth, and the thing certain, that such abomination is wrought among you;
15 Thou shalt surely smite the inhabitants of that city with the edge of the sword, destroying it utterly, and all that is therein, and the cattle thereof, with the edge of the sword.
16 And thou shalt gather all the spoil of it into the midst of the street thereof, and shalt burn with fire the city, and all the spoil thereof every whit, for the LORD thy God: and it shall be an heap for ever; it shall not be built again.
Deuteronomy 20
16 But of the cities of these people, which the LORD thy God doth give thee for an inheritance, thou shalt save alive nothing that breatheth
Either these books are lies (leaving nothing supporting claims about god) or you believe that god commands genocide from time-to-time (in which case you are sick and need professional help). I've read the apologetics and they should sicken any rational human being.

If these passages are taken to be historical, then men took swords and SLICED OPEN infant after infant after infant. To even HINT that a god would command such a thing is the most vile lie ever to leave mans lips or his quill. It sickens me to think of the atrocities that men have committed solely because it was CLAIMED that god willed it so. And no, it is not a sufficient defense to claim that these children will go to an imaginary heaven - so that makes it ok. Reverse the situation - have someone murder YOUR CHILD and THEN I want to see you excuse their actions because your child will go to heaven. You KNOW it's wrong.

Various (unsubstantiated) claims have been levied at these people in order to try to justify the atrocities apparently commanded by god in the bible. They worshiped a different god, they had the wrong kinds of sex with each other, they didn't love the way the authors of the bible thought people should love, they committed child sacrifices (kind of like god supposedly commanded of Abraham? IF they were committing child sacrifices then WHY didn't god just intervene in the Hittite ritual like he did for Abraham? Clearly he CAN if he feels like it). But no, this time god said the punishment for those adults who had committed these sins was for their CHILDREN to be hacked to pieces with a sword - and wasn't that a convenient justification for those who would take their land afterwards? I call such a god utterly unworthy of worship. If that really IS the god that exists then it is no wonder his own creations supposedly revolted against him.

I prefer to think that reality is not nearly that evil or stupid. I don't think there is a god at all, least of all a personal god as concieved by warmongering, goat herding, misogynists.

I have no issue with someone who wants to believe in a good higher power as long as they STOP there - once you start making claims about what this god commands or wills then you better have something better than 3000 year old drek about a war god who wills humans to stone each other to death, cut off part of their child's genitalia, and murder entire populations of other people because they are 'bad' (without ever enumerating any crimes which could possibly morally justify such an atrocity).

And you DARE to ask where MY morals come from? -- I ask where YOUR morals come from because they are clearly lacking. My morals come from the evolutionary processes which yielded my ability to observe and predict the consequences of actions. The fact that I CAN make reasoned choices based on knowledge and prediction is what gives me the moral responsibility to make some choices over others.

Don't get me wrong, I don't mean to be picking on Judaism here - Christianity and Islam are all equally vile -- Their disgusting and all too human treatment of one another should be all the evidence anyone needs that there is no god at work behind any of these religions.

You don't need a god to exist to see that we need to work together to make the world a better place for our selves and our children. I applaud all those good people who have been deluded by the call of religious surety and false promises of justice and peace only in a future world and yet remain good people in spite of it. And I condemn all those people who commit ill, some in the name of religious dogma and some in the name of ideological dogma - but all as a result of fallacious logic, incorrect facts, and a fundamental lack or denial of their own humanity.

I do not believe in god but I HOPE a god exists - a just and moral god that had nothing to do with Judaism, Christianity, or Islam. If I am to be punished for trying to live a good life and being HONEST about the evidence before me, then so be it - I welcome it because I would have NOTHING to do with such a petty, jealous, petulant god.

And I do not wish to scapegoat the punishment for my sins onto another either. I'll have nothing to do with the cannibalistic and sick worship of the torture and murder of another human being whom was (at best) mislabeled Christ. [There is simply not sufficient evidence to believe a Jesus person actually existed as described in the Christian bible - but neither is there sufficient evidence to support the claims of Exodus].

So yes, I believe I am more moral than the average religious person BECAUSE I refuse to accept some foolish authority which makes blatantly HORRENDOUS claims about what is supposedly moral.

I have sound logical justifications for my ethical beliefs AND I am open to questioning them in light of new evidence or argument. The crime of the religious believer is that they form their ethical beliefs in a near vacuum of data (save the appeal to authority of some book) and then proceed to commit crimes against humanity wearing the blinders of righteous indignation. Nothing makes a non-believer more sure of their choices than the statements and action of such a hypocrite.