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.

Genetic Engineering Algorithms

Why do I care?

In discussion with creationists, I'm often told that "randomness cannot design." 

No. ToE is based on random mutation... Randomness cannot design. @StuDiligence @BigBangOrBigLie pic.twitter.com/M8JNnJ2lqR

— Rabid Dan (@DanThaWildMan) November 19, 2015

@DrJ_WasTaken
Flight cannot arise gradually with random mutation/natural selection@apostolicfdn @DynoJJ @RJDownard @TamiHoshiyama

— Preacher (@_OnlineGospel_) November 4, 2015

That's utter bullshit. One of the ways I reply to these tweets is with examples of Genetic Design Algorithms, where random mutations coupled with selection and reproduction based on objective performance criteria can will always result in the appearance of design that satisfy the performance criteria.
In the course of these conversations, I've dug up quite a few resources and developed a few memes.

Evolution Works

It works so damn well that it can be used to design things when you're not sure what approach is best. I'm not just saying that, there's really good examples:

• Field -Programmable Gate Arrays (FPGA's) have been designed to distinguish sounds. 
• There are countless other examples in the literature of successful genetic design algorithms dating back over 20 years.
• There are commercial software products like Genetic Designer and Natural Selection which provide tools for genetic design
• Open-source libraries are free and available, so you can study the techniques and evaluate the performance for yourself. Admittedly, most of the people don't have the technical expertise, time, or patience to learn how to use these tools.

Watch it Happen Yourself

There are some really great examples of genetic design algorithms which can be watched evolving in near-real-time. One of my favorites is called BoxCar2D. In it, you can watch randomly designed cars compete for speed and distance.  Successful cars reproduce with random mutations. You can even manipulate the mutation rates and number of top cars to breed. BoxCar2D is a pretty robust simulation,
There are other, simpler online examples of the same basic concept. Since they're simpler, they converge faster:

• Genetic Algorithm 2D is a version that runs on pure HTML5 / javascript, so you don't need Flash.
• Genetic  Cars lets you cross-breed your cars with cars from other online players.
• Darwin Bots is a more comprehensive simulation that runs on your desktop
• BioMorph is a simulator where the user interactively selects the successful child in each generation.

I'm sure there are more. If you have a personal favorite, please post a comment or tweet me.

Check Your Ego Before You Say Science is Wrong

Science is a process of constantly facing challenge by experts to validate the reliability of results and
conclusions. I trust the scientific process to reach the best possible answers on all matters to which it applies.
To suggest that a layman can out-think the international scientific community or has uncovered a "flaw" in scientific consensus is almost impossible. This happens most often when science is politicized: global warming, vaccines, and evolution come to mind.
There are many sources of cognitive bias to which we are all subject, but the relevant one here is called the "Dunning-Kruger" effect. Simply put, it states that before we understand a technical field, we are likely to underestimate its complexity and therefore overestimate our own abilities in the field. In short, it's arrogance -- unwarranted confidence in our own abilities.

So check your ego before you claim to know that science is wrong.

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.

An Observation on Evolution Debates

Note: Some of this was written as if addressing a creationist. 

Charles Darwin, author of Origin of Species, is NOT the only scientist ever to study evolution.

Whether evolution is valid or not isn't really a question which anyone is going to prove as laymen in an Internet debate. The real issue here is who should we trust for an understanding of the world. I've been debating with evolution deniers first several months now, and I have yet to meet one who can actually explain with the claims of evolution actually are. The "Evolution" being rejected is not actually evolution, but a strawman presented by preachers in an attempt to discredit science.

I accept the consensus conclusion of tens of thousands of independent international scientists around the world. These scientists actually studied evidence from many different disciplines, to include:

• Radioisotope dating
• DNA comparisons on living species
• Morphological comparisons of living animals 
• Morphological comparisons of embryonic development
• Detailed catalogs of skeletal evolution, including temporal information from radioisotope dating, geographic information which shows the moron of the species, and eventually modern day ancestors of the skeletal remains. 

As a scientist, I seek out criticism of my work. Peer review is there to ensure I'm not reaching conclusions that are unsupported by the evidence or misinterpreting evidence that I've reviewed. Carefully criticizing my peer's work is one of my responsibilities — essentially, looking for potential holes or gaps in my case. That's how science works.

Authority is not worth much in science. A famous scientist may get more frequent invitations to be the keynote speaker, but her academic presentations and papers must continue to stand on their own merits. In fact, many audience members or paper reviewers become more critical for a famous scientist's work out of a desire to appear smarter. 

When a creationist claims the mainstream scientific consensus is wrong, they're essentially claiming that the scientific process has not only failed, but that it continues to fail. And it does this not for a single research laboratory, but for the entire biological and paleontological branches of science. That the scientists who have dedicated their lives to the careful study of a narrow aspect of biology or paleontology is somehow fatally flawed. That gaps and erroneous assumptions have somehow gone undetected. And if that isn't absurd enough, these gaps and flaws must persist across the study of many different species, by scientists from many different institutions and countries.

A phylogenetic tree of life, showing the relationship between species whose genomes had been sequenced as of 2006. The very center represents the last universal ancestor of all life on earth. Note the presence of Homo sapiens (humans) second from the rightmost edge of the pink segment.

The sheer magnitude and absurdity of this claim of scientific community ineptitude is difficult to grasp.  The figure at right is a dramatically simplified view of the tree of life as determined by sequencing modern genomes. While consolidating this information and constructing the tree via statistical analysis may have been the work of a couple teams of scientists, the supporting collection of evidence and extraction of genetic data was supported by many different scientific teams.  Though the branches in this figure are developed by statistical clustering models (likely k-means), they match the branches of phylogenetic classification of modern species and fossil records. Independently, either one of these two approaches to classification of species is compelling evidence for evolution. Taken together, with the understanding that they agree, is overwhelming evidence. If a god created these creatures as we see them, it must be a trickster god, trying to deceive us into believing evolution. 

I'm not able to conceive of a means by which this could happen.There are clearly smart people working at ICR and AiG to attempt to discredit the theory. Rather than starting with the evidence and considering several possible conclusions, these "scientists" start with their conclusion (biblical "Truth™") and work to find confirmation for it in the observable world. This approach is fundamentally dishonest. Yet their work has had little or no impact on biology or geology. Their findings are reviewed and dismissed as invalid or irrelevant. If there were valid points to their claims, they would be recognized by a the scientific community.

References:

1. By Ivica Letunic: Iletunic. Retraced by Mariana Ruiz Villarreal: LadyofHats [Public domain], via Wikimedia Commons
   Caption: A phylogenetic tree of life, showing the relationship between species whose genomes had been sequenced as of 2006. The very center represents the last universal ancestor of all life on earth. The different colors represent the three domains of life: pink represents eukaryota (animals, plants and fungi); blue represents bacteria; and green represents archaea. Note the presence of Homo sapiens(humans) second from the rightmost edge of the pink segment. The light and dark bands along the edge correspond to clades: the rightmost light red band is Metazoa, with dark red Ascomycota to its left, and light blue Firmicutes to its right.