Response to Evolution "News"

I don't know why I wasted my time. My edits are in bold italics. Response to 

http://www.evolutionnews.org/2015/09/waiting_for_mut099631.html

Many (hardly any) scientists now recognize the insufficiency of the classic Darwinian story to account for the appearance of new features or innovations in the history of life. They focus on other theories to account for remarkable differences between genomes, the appearance of novel body plans, and genuine innovations like the bat's wing, the mammalian placenta, the vertebrate eye, or insect flight, for example (In the same way that General Relativity improved on "Newtonian Theory" and made Mercury's orbit work?). They realize (Inspired by their religion, they believe) that the traditional story of population genetics (changes in allele frequencies in populations due to mutation, selection, and drift) cannot account for "the arrival of the fittest" and not just the "survival of the fittest." (Hugo DeVries, 1904). <--  Wow, they're reaching DEEP into the historical academic work

One of the reasons many (this tiny fraction of )scientists acknowledge the insufficiency of Darwinism is because they know the refuse to admit that the accounting won't works. The mutation rate, the generation times, the strength of selection versus genetic drift, the population sizes, and the time available don't match up just fine.

Here's where they deliberately misinterpret journal results and compare apples to oranges to make the reader think there's something wrong with science. At its core, this is part of a larger argument from ignorance approach, paraphrased as: 'Science isn't right. Therefore God did it.'

For example, supposedly humans last shared common ancestry with chimps about six million years ago. Since that time, we have accumulated significant differences with chimps -- genetic, anatomical, physiological, behavioral, and intellectual differences, among others. The genetic differences between humans and chimps are much more than the (shrinking) 1.2 percent difference in base pairs that is so often quoted in the media. (Yes, there are different ways of measuring similarity.) Add small insertions and deletions and the differences climb to about 3-5 percent,depending on whose estimate is used. Add another 2.7 percent for large scale duplications or deletions, another 6 percent for new Alu elements (a kind of mobile genetic element) and some unknown number for rearrangements of the DNA, other insertions of mobile genetic elements, or new genes, we have more than 11.7 percent of our genome with unique features not present in chimps. (Only when you struggle to exaggerate moves and deletions. For reference, here is the preliminary analysis as published in Nature.) 

There is only so much time for these differences to have accumulated. Mutations arise and are propagated from generation to generation, so the number of generations limits how many mutations can accumulate. The estimated mutation rate is about 10^-8 per base pairs per generation, and we have an average generation time of somewhere between 10 and 25 years. Our estimated breeding population size six million years ago is thought to have been about 10,000 (these are all rough estimates based on numbers currently in use -- see the papers cited below). Based on these numbers, one can estimate how many years it would take to acquire all those mutations, assuming every mutation that occurred was saved, and stored up. (Since the mutation rate is extremely small and uniformly distributed, this assumption is valid.)

But there's a difficulty -- it's called genetic drift. In small populations, like the 10,000 estimate above, mutations are likely to be lost and have to reoccur many times before they actually stick (WTF? It's not like a specific change keeps trying. Many are just lost). Just because of random effects (failure to reproduce due to accidental death, infertility, not finding a mate, or the death of all one's progeny), a particular neutral mutation may have to arise many times before it becomes established in the population, and then many more years before it finally becomes fixed (that is, before it takes over the population and replaces all other versions).

What a strange misinterpretation of the process! The author seems to think that the mutations which fail to reproduce keep trying until they stick. Bizarre! Clearly, lost mutations are simply lost. Just like the 99.9% of all species which have gone extinct. Very few succeed.

How long before a single, new mutation appears and becomes fixed? An estimate from a recent paper (by a Young Earth Creationist) using numerical simulations is 1.5 million years. That is within the range of possibility. (By assuming that there is only a single specific desirable mutation being considered by nature at any given time.) But what if two specific mutations are needed to effect a beneficial change? Their estimate is 84 million years. Other scientists have done this calculation using analytical methods, but their numbers are even worse. One report calculates 6 million years for one specific base change in an eight base target typical of the size of a DNA binding site to fix (In the abstract, the author points out that the sequence needn't be perfect to be valuable, reducing the time to 60,000 yrs), and 100 million years to get two specific mutations. (That work was later amended to 216 million years.) Extrapolating from other published data merely confirms the problem.

Astonishing dishonesty! A brief review of the linked article (100 million years) contains the following quote: "Fortunately, in biological reality, the match of a regulatory protein to the target sequence does not have to be exact for binding to occur. Biological reality is complicated, with the acceptable sequences for binding described by position weight matrices that indicate the flexibility at different points in the sequence. To simplify, we assume that binding will occur to any eight-letter word that has seven letters in common with the target word. If we do this, then the mean waiting time reduces to ∼60,000 years."  Why would Evolution "News" need to misrepresent the author's conclusions in their linked article? Did they think nobody would read it?

Durrett makes a good analogy to the mistake Michael Behe made to reach is 216 million year figure in the linked article: "Behe is not alone in making this type of mistake. When Evelyn Adams won the New Jersey lottery on October 23, 1985, and again on February 13, 1986, newspapers quoted odds of 17.1 trillion to 1. That assumes that the winning person and the two lottery dates are specified in advance, but at any point in time there is a population of individuals who have won the lottery and have a chance to win again, and there are many possible pairs of dates on which this event can happen. The probability that it happens in one lottery 1 year is ∼1 in 200 (Durrett 2009)  

Another paper came up with much shorter time frames by assuming that any 5 to 10 base pair binding site could arise anywhere within 1 Kb of any promoter within the genome. 

Yet in all likelihood many more than two binding sites would be required to change anything significant, and those binding sites must be appropriate in location and in sequence to accomplish the necessary changes. They must work together in order for a specific adaptive change to happen.  (Again, the authors seem to think that these changes are prescribed and can't be happening at random, in parallel, and at different sites.) 

Genes operate in networks, and to shift a gene regulatory network would require many mutations, and not just random ones. Remember there are anatomical physiological, behavioral, and intellectual differences to explain, multiple traits each requiring multiple coordinated mutations. Unless one invokes luck on a large scale, those traits would not have come to be. (Again, all this presumes humanity is the intended end-state. It is because it is.) 

I'm not betting on luck. (Of course you're not). 

Image: Homo georgicus, reconstruction, photo by 120 (Own work (photograph), model by Élisabeth Daynes) [CC BY-SA 3.0], via Wikimedia Commons.

Well that was as much fun as beating my head against a wall. The basics mistakes are as follows:

1. Cite ancient journals from 1904 as if they're still relevant
2. Misrepresent the number of changes
3. Cite letters to journals which explicitly refute the point you're claiming they make (oops?!)
4. Presume that the genetic changes were prescribed
5. Assume intelligent humanity was the universe's desired end-goal
6. Ignore that a neutral genetic change will not survive without a second change that's necessary to the benefit. Indeed, we could have millions of such single-mutations waiting on a second mutation to confer a benefit.

Ideas for an atheist billboard near the Ark Encounter

We need your inputs.

I'd like to see atheist (or maybe just rationalist) advertising near Ken Ham's monument to ignorance and genocide (A.K.A. "The Ark Encounter") but I'm not sure where to start or what the right message should be. Here are some ideas:

• Did it rain in Antarctica?
• How did all the marsupials get to Australia?
• What did all the animals to to deserve death?
• How many babies drowned in the "flood"?
  Good thing it never really happened.

There's more detailed arguments against it but they involve some math, which requires some thought that doesn't fit in the freeway-Billboard timeline.

My goal would be to plant some seeds of doubt in the minds of those attending. Other ideas are either more abrasive or more mathematical.

• Does your God commit genocide?
• Need to fact check this: Most Jews and Most Christians understand the Ark is a myth. (Optional: But most Muslims accept it as truth.)
• Show a valid quote from a Pope stating that the Ark is a legend, "Even the pope admits it never happened"
• Where did the food come from? Where did the poop go?
• Fire code limits Ark Occupancy at X. That's only X/2 species.

Goals of such a sign:

• Raise awareness that lots of people think this is absurd
• Advertise an atheist / secular / skeptical event (leverage media coverage as advertising)
• Plant a seed of doubt in the indoctrinated
• What else could we accomplish? Not gonna convert anyone.

In any case, I think a WAG for such a billboard is about $5k. Not sure if that includes the design or not. Please share this article if you'd support the idea. And share your thoughts in the comments section below or via tweet to @AtheistEngineer.

Edits and Updates:

• If at first you don't succeed …
  Drown everything and try again [link]
• "Would a loving and all-powerful god REALLY annihilate all of humanity on the planet for the purpose of a do-over?" [link]
• We don't celebrate death (images of Ark, Abraham/Isaac, Passover, and Jesus).
  Atheists are better without gods.
  Meet-up / event information.
• Ark Encounter: Were the only evidence necessary is proof of admission. [link]
• "Ark Encounter": Science-free zone ahead [link]
• "Ark Encounter": Proven wrong by geology, archaeology, genetics, and common sense
• If you think Noah and his family cared for millions of animals, you've quite obviously never kept a horse.... [link]
• Rear view: God carrying set of golf clubs walking toward the "19th hole" caption reads: Noah's Ark: God's Mulligan [link]
• Noah's Ark: Why would you want to spend eternity with the worst mass murderer in "history"?  [link]
• @AtheistBigfoot: @AtheistEngineer The passage should be "Others will know this BS is crazy, but not you. You're gullible" 
• @wildy412: @AtheistEngineer want to drop out of school, stop thinking for yourself? Visit the Ark, where stupidity welcomes you.

Why Louis Pasteur Didn't Prove Abiogenesis is Impossible

Christians often like to claim that Louis Pasteur proved abiogenesis was "impossible."  Here's the first example I came across in my search. It's a pretty professional-looking production. And it's short, so you won't hate me for wasting much of your life if you watch it. Seems like these guys understand the science and have thought it through, right?

Louis Pasteur in his laboratory.

A more careful review of his work demonstrates that he most certainly did nothing of the sort. In his experiment, Louis Pasteur experimented with relatively small quantities of liquid compared to the volume of liquid on earth. Let's pick an absurdly large number in order to give the Christian claim every possible benefit.  Suppose that Pasteur tested a thousand cubic meters of liquid. That's 260,000 gallons, larger than the Giant Ocean Tank at the New England Aquarium. Pasteur demonstrated that no life spontaneously generated in them over the course of his experiment. Let's assume that it was a decade-long experiment.  These would be very large numbers, considering the pictures available of him in his laboratory.  Pasteur's analysis did not demonstrate that life never spontaneously forms anywhere ever. It only showed only that life did not spontaneously generate in the large sample of broth over the time period he tested.  This puts a lower-bound on the mean time until life spontaneously forms in a given volume of liquid.  In other words, we can say with confidence that life sponteneously generates less often than once in $10^4 m^3  \cdot years$ . (for the sake of simplicity, I'm presuming that the spontaneous generation of life would follow Poisson distribution where each infinitesimal unit of liquid volume is as likely as any other to spontaneously generate life per unit time).

Now, compare that volume to the volume of water on earth ($1.386 \times 10^{18} m^3$) and we can then calculate a lower-bound on the global spontaneous generation rate:

$ f_{gen} < \frac{10^4 m^3/yr}{1.386\times 10^{18} m^3} $

$ f_{gen} < 1.386  \times 10^{14} year^{-1}  $

$ f_{gen} < 4.39 MHz $ [ref] 

That's right.  Pasteur's experiment shows that life spontaneously forms on Earth at a rate below 4.4 million times per second.  And that's with the generous assumption that he tested a thousand cubic meters of solution! Life could be forming all around the world at a rate of 4.4 MHz, and Pasteur's experiments would remain a valid measure. In 1000 cubic meters over a decade, life is unlikely to form.

The Farcical Fables of Answers in Genesis

The Crystal King in Ohio Caverns would take 200,000 years to form at today's growth rates.

Science literacy is important to me. This massive stalactite we saw in the Ohio Caverns yesterday would take 200,000 years to form (at today's growth rate). It couldn't have started forming until after the cavern was eroded away. One of many, many examples requiring extensive mental gymnastics to fit into a young earth creationism model, but which is explained simply once we accept the earth is 4.54 billion years old.

It's funny to watch dishonest organizations like Answers in Genesis do the extensive mental gymnastics to make a story that sounds plausible. Here's a rather pathetic attempt to address Cave Formations by AiG that is worth a read for its humor value. Some key failures of their farcical story-telling:

• Limestone formed in the massive flood
• Stalactites formed very quickly, then slowed down by several orders of magnitude, and now appear constant.
• Fossils were buried catastrophically, but in the same order all over the world?!
• Look how they use the word "evolution" as a childish insult. WTF is an "evolutionary geologist?!!!" I think they mean "geologist". Evolution has NOTHING TO DO with geology, but I've heard people make such a claim before and now I understand where it came from.

The lengths these people go to is laughable, but the sad part is that their mission involves spreading the unsubstantiated, untested, and unverified story as if it were fact to children and adults who honestly don't know any better. Answers in Genesis is like the Onion or the Free Wood Post, but without the disclaimer that it's satire.

Update on AiG's Frivolous Lawsuit

A Couple weeks ago, I posted a blog entry criticizing Answers in Genesis for filing a frivolous lawsuit in response to the Commonwealth of Kentucky denying their request for special Christian privileges. In short, AiG asserts they are entitled to special tax incentives for their first ever theme park to celebrate an act of mass-genocide (The Ark Encounter), despite the fact that as a bigoted religious organization, they intend to discriminate in employment based on religion, sex, and sexuality.

The intellectual dishonesty of AiG just pisses me off. It's one thing to have crazy religious beliefs. It's fine to build a theme park to genocide if that's what your horrific "god" demands of you. But to misrepresent the facts and accuse the state of "religious discrimination" is appalling. In a video released by the organization, Lawyer Mike Johnson, says, “Religious groups, ideas, and organizations can’t be treated with hostility by the government." Apparently, it's "hostility" to deny tax incentives to organizations that intend to discriminate?! This is Christian privilege and persecution complex at its finest.

Despite AiG's stated intention of serving only a select group of ignorant Christian conservatives within the Commonwealth of Kentucky, AiG apparently believes that Kentucky taxpayers should foot the bill for their theme-park-celebration-of-death. Just take a look at the artwork on their announcement page (right). It's a guy behind bars! As if to suggest that the "religious discrimination against Christians" is Kentucky is rounding up and arresting Christians?! The trumped-up persecution complex is just astonishing. How can anyone take this organization seriously?  It's not religious discrimination to reject your tax break when your organization plans to discriminate!

Tax breaks are for organizations that better the whole community, which AiG decidedly does not. Sorry AiG, but if you want the tax incentives, you'll need to serve everyone. Not just the heterosexuals; not just the protestant Christians. You'll have to hire and admit the the following groups of people to your theme-park-of-destruction:

• Gays
• Fornicators
• Catholics
• Jews
• Muslims
• Apostates
• Mormons
• even … Atheists (!!!)

AiG Files Frivolous Lawsuit Over Not Getting Their Christian Privilege

Here's their press release:

• https://answersingenesis.org/religious-freedom/religious-discrimination-lawsuit-filed/

I'm sorry, Ken Ham, but it wasn't "religious discrimination" that led the state of Kentucky to reject your request for a tax incentive.  It's that your bigoted Answers in Genesis organization intends to discriminate in its hiring based on religious affiliation and sexuality.

You can't have it both ways, Ken. If you want our secular society to invest in the success of your monument to mass genocide, you'll need to demonstrate that the economic benefit will support all citizens, not just your fellow religious kooks.  So build your homage to horrific destruction with the money you bilked out of the gullible. But don't come asking us for a hand out.

And fuck you for wasting our money on a frivolous lawsuit.