Sunday, July 31, 2011

A response to a Catholic

Posted At: http://www.ncregister.com/blog/5-catholic-teachings-that-make-sense-to-atheists/
@LAJ Thank you for your reply, this is more interesting discussion than most :)
"intent on misreading the Bible" a very nice general dismissal, but lacking substance. Where did I misrepresent what's in the Bible? Pick one and we will discuss it because I assure you I have read the whole thing at least once and done extensive research on many passages. I'm not some random atheist - I'm a former Christian and I was prepared to thoroughly dedicate my life to God at one point in my life.

I note with sadness that you didn't address the link about the immobility of the Earth. Something that disproved the bible 400 years ago. How do you rectify that in your mind? Most Protestants merely excuse it as Catholic nonsense, but as a Catholic you are kind of stuck with it since you believe in apostolic succession it is irrational to believe that something that was so fiercely held could be so wrong. This since fact alone does in the entire biblical structure for me.

Thursday, July 28, 2011

Strong religeous convictions

Found on: http://deepakchopra.com/2011/07/the-american-melting-pot-atheists-keep-out/
"those who had the courage to travel to new lands,mostly didso on the back of strong religeous convictions"

Let's not forget that "strong religious convictions" includes Columbus, Ponce de Leon, Panfilo de Narvaez, Hernan Cortés, Francisco Pizarro... all Christians, all well-known murders and enslavers of uncountable numbers of indigenous people.

Dr. Michael McDonnel wrote in The 'Conquest' of the Americas:
conquistadors regarded plunder, slaves, and tribute as the just desserts for their efforts in forcing pagans to accept Christianity and Spanish rule. After all, the conquistadors did scrupulously adhere to the Spanish law of conquest by reading the requerimiento, which ordered defiant Indians to immediately accept Spanish rule and Christian conversion, or face punishment in a “just war”. The requerimiento announced that “The resultant deaths and damages shall be your fault, and not the monarch’s or mine or the soldiers”. Attending witnesses and a notary usually certified in writing that the requerimiento had been read and ignored by the usually uncomprehending Indians, thus justifying the death and destruction that so often followed.

Saturday, July 23, 2011

Google+ suspended

Well, it happened as I feared, Google+ has suspended my profile (for not using my real name I believe).

Sunday, July 10, 2011

But I Had A Personal Experience!

Why we cannot rely solely on individual memory to document events.

Remarkable false memories By Daniel Simons

I myself have personally had some pretty amazing experiences and witnessed amazing phenomena as products of meditation (and on occasion, medication). I have SEEN a golden, radiant book with letters of fire burning onto the pages (meditation), I have seen images of the future that have subsequently come to pass (lucid dreaming, meditation), and I have been 'miraculously' saved from physical harm (reality). Be they coincidences, hallucinations, lucky guesses, or who knows, maybe even some quantum process that we don't understand yet. But not a SINGLE one of those experiences is evidence for something supernatural or a soul. The dreaming brain is perfectly capable of generating PROFOUNDLY meaningful and deep, rich experiences that are indistinguishable from reality to the observer. I know this because I practiced at it for many years.

Saturday, June 25, 2011

RESPONSE: Galileo rout: Galileo rout

RESPONSE: Galileo rout: Galileo rout

The referenced page is just absurdly incorrect and a very simple thought experiment will demonstrate this very clearly.

The orbital circumference of the moon1 is 2,413,000,000 meters, and the average orbital velocity is 1022m/s, dividing circumference/velocity gives us ~27.327 days2. This is how long it actually takes the moon to go ALL THE WAY around the Earth in its orbit.

But when we observe the moon it appears to go all the way around the Earth every single day, it doesn't take 27.327 days! If the Earth were NOT rotating then we would see the moon only move 1/27.327th of the way across the sky in a 24 hour period.

So the hypothesis proposed is clearly and demonstrably false.

Friday, June 24, 2011

RESPONSE: Atheism?: Is It Real?

RESPONSE to Atheism?: Is It Real?

The bible also says 'ye shall know them by their fruits'.

So which of the 30,000 some odd sects do you believe is the RIGHT one so that we can discuss your specific beliefs?

Since they all have different beliefs that conflict with the others they cannot ALL be right - so that is a LOT of bad fruit.

How do you KNOW that you have the exact right version of beliefs?

You seem to think you are saved by faith alone but others disagree with you. Are you SURE you aren't saved by works?

When I look at the FRUIT of religion I see begging liars on TV asking for money, I see wealthy immoral church leaders, I see child raping priests, I see FLOCKS of people who shut their mind and harden their hearts against their fellow humans and try to deny them civil rights. They are racists and bigots.

1 Peter 2:1 Therefore, rid yourselves of all malice and all deceit, hypocrisy, envy, and slander of every kind.

Has YOUR church done all these things?

I see fraud, slavery, theft, murder, hatred, sectarian violence around the world, all directly because of religious COMMANDS. Not just because there are bad apples in the bunch, DIRECTLY because of the commands and edicts of their religion.


Columbus, Ponce de Leon, Panfilo de Narvaez, Hernan Cortés, Francisco Pizarro... all Christians, all well-known murders and enslavers of uncountable numbers of indigenous people.

Bernal Diaz wrote of the sack of the Aztecs, that “When the Christians were exhausted from war, God saw fit to send the Indians smallpox, and there was great pestilence in the city.”

Dr. Michael McDonnel wrote in
The 'Conquest' of the Americas:
conquistadors regarded plunder, slaves, and tribute as the just desserts for their efforts in forcing pagans to accept Christianity and Spanish rule. After all, the conquistadors did scrupulously adhere to the Spanish law of conquest by reading the requerimiento, which ordered defiant Indians to immediately accept Spanish rule and Christian conversion, or face punishment in a “just war”. The requerimiento announced that “The resultant deaths and damages shall be your fault, and not the monarch’s or mine or the soldiers”. Attending witnesses and a notary usually certified in writing that the requerimiento had been read and ignored by the usually uncomprehending Indians, thus justifying the death and destruction that so often followed.

Well, Thank GOD they followed protocol before they murdered, raped, and enslaved entire populations. That makes it ok, right?


The http://en.wikipedia.org/wiki/Requerimiento was "used to justify the assertion that God, through historical Saint Peter and appointed Papal successors, held authority as ruler over the entire Earth; and that the Inter Caetera Papal Bull, of 4 May 1493 by Pope Alexander VI, conferred title over all the Americas to the Spanish monarchs"


But that's not YOUR religion, that was the "Catholics" so that doesn't count, right? They have it all wrong. Of course, they claim YOU have it all wrong, you have broken away from the one true Church, you know, the one founded by Jesus and Peter...

17 Jesus replied, “Blessed are you, Simon son of Jonah, for this was not revealed to you by flesh and blood, but by my Father in heaven. 18 And I tell you that you are Peter,[b] and on this rock I will build my church, and the gates of Hades[c] will not overcome it.

The Church put in the hands of Peter (who's name means the rock), handed down through apostolic succession.

And still, so many rotten fruits...

Minds so rotted by this stinking fruit that they can look at tens upon tens of THOUSANDS of scientific papers that all evidence and affirm that evolution is true, but they still deny it.

Minds so rotted by this stench of ignorance that they ignore that the heliocentric nature of the solar system PROVES the bible is false.

Both Paul V and Urban VIII KNEW the damage this information could do and suppressed this information to the point of burning Giordano Bruno to death over it. They greatly underestimated the credulity of their flock.

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

http://web.me.com/atlwx/wxhistory/files/20070501-drought.html
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: http://www.gawrc.org/2011paper_pdfs/7.3.4Kim.pdf

See also: http://ga.water.usgs.gov/

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.

Overview


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.