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Evolutionary Genomics Programmer Position Available

Posted 27 January 2016 by Reed A. Cartwright

The Human and Comparative Genomics laboratory at the Biodesign Institute is looking for a Software Application Associate who will work in a collaborative environment to design, construct, test, document and maintain software packages. Typical projects involve implementing high performance algorithms for the statistical analysis of large genomic datasets for studying questions related to evolution and population genetics. To apply visit http://links.asu.edu/job19991BR or search for ID 19991BR at https://cfo.asu.edu/hr-applicant. If you have any questions about the opening, please email cartwright@asu.edu and visit http://cartwrig.ht/. ESSENTIAL DUTIES: Develops and documents requirements of software applications. Participates in on-the-job and formal training sessions concerning the design, writing, and testing of software application programs. Participates in and/or independently performs the design, testing, and documentation phases of programs. Translates predetermined logic into appropriate programming language and operating systems. Utilizes standard reference, resource, and/or procedural materials to resolve problems. Integrates multiple tools into a single, user-friendly software package, as well as providing support for the software. Operates on-line terminals and related computing equipment as required. MINIMUM QUALIFICATIONS: Bachelor's degree in Statistics, Mathematics, Computer Science or related field AND two years of experience in software application development, including writing computer code in one or more programming languages; OR, any equivalent combination of experience and/or education from which comparable knowledge, skills and abilities have been achieved. DESIRED QUALIFICATIONS: Experience in translating software prototypes from Perl, Python, Java, etc into C/C++ preferred. Experience with JavaScript. Experience with databases query tools including, but not limited to, SQL, as well as programming languages including, but not limited to, C++ python, XML, HTML. DEPARTMENT STATEMENT: The Biodesign Institute addresses today's critical global challenges in healthcare, sustainability, and security by developing solutions inspired from natural systems and translating those solutions into commercially viable products and clinical practices. The Cartwright Lab is based in the Human and Comparative Genomics Laboratory in the Biodesign Institute at Arizona State University. Our research focuses on various topics in the field of computational evolutionary genetics. We develop methods and software to analyze large genomic datasets and "big data". The majority of our research is related to the detection and analysis of mutations and variation from next-generation sequencing. We are species-neutral and work on taxa across the tree of life. Recent work involves humans, cancer, bonobos, ciliates, maize, Plasmodium, Leishmania, E. coli, archaea, Solanaceae, strawberries, and Anolis.

75 Comments

Joe Felsenstein · 27 January 2016

I guess you'll have to hire one of the regular commenters at Uncommon Descent. Because, as they regularly assure us, they are the hard-nosed folks who know how to deal quantitatively with biology, while we biologists refuse to do any quantitative analysis of biology at all. We just endlessly tell tall tales and spend our time talking about what Darwin did and said, and saying how great Darwin was and how everything he did was free of error.

So there is your only possible pool of candidates, since no biologist has ever used a computer.

Mike Elzinga · 27 January 2016

Joe Felsenstein said: So there is your only possible pool of candidates, since no biologist has ever used a computer.
It's hard to forget the total confusion a couple of years ago among the denizens of UD in trying to get even Dawkins' little Weasel program to work. It provided a few good chuckles and eye-rolls.

DS · 28 January 2016

Well if you require applicants to sign a statement of faith, maybe you can get some tax breaks. Maybe something like:

"I believe in the holy law of evolution and the science for which it stands. One nation, under Canada, with technology and progress for all."

Well you can work on that, but you get the idea.

Wallace Barbosa de Souza · 10 February 2016

Joe Felsenstein said: I guess you'll have to hire one of the regular commenters at Uncommon Descent. Because, as they regularly assure us, they are the hard-nosed folks who know how to deal quantitatively with biology, while we biologists refuse to do any quantitative analysis of biology at all. We just endlessly tell tall tales and spend our time talking about what Darwin did and said, and saying how great Darwin was and how everything he did was free of error. So there is your only possible pool of candidates, since no biologist has ever used a computer.
As a biologist, would you answer me the following questions with empirical support: How did genomes evolve? How do stochastic mutations are able to generate long strands with millions of correctly ordered nucleotides along with the inseparable proteic machinery that replicates, unzip, translate and repair the genome, not to mention the networks of several classes of RNAs and ncRNAs that play many crucial roles? Thank you in advance.

Mike Elzinga · 10 February 2016

Wallace Barbosa de Souza said: How do stochastic mutations are able to generate long strands with millions of correctly ordered nucleotides along with the inseparable proteic machinery that replicates, unzip, translate and repair the genome, not to mention the networks of several classes of RNAs and ncRNAs that play many crucial roles? Thank you in advance.

Mike Elzinga · 10 February 2016

Wallace Barbosa de Souza said: How do stochastic mutations are able to generate long strands with millions of correctly ordered nucleotides along with the inseparable proteic machinery that replicates, unzip, translate and repair the genome, not to mention the networks of several classes of RNAs and ncRNAs that play many crucial roles? Thank you in advance.
Just out of curiosity; could you explain what you mean by "stochastic mutations" and why you think atoms and molecules cannot evolve into complex structures? I suspect you have some specific calculation in mind.

Wallace Barbosa de Souza · 10 February 2016

Mike Elzinga said:
Wallace Barbosa de Souza said: How do stochastic mutations are able to generate long strands with millions of correctly ordered nucleotides along with the inseparable proteic machinery that replicates, unzip, translate and repair the genome, not to mention the networks of several classes of RNAs and ncRNAs that play many crucial roles? Thank you in advance.
Just out of curiosity; could you explain what you mean by "stochastic mutations" and why you think atoms and molecules cannot evolve into complex structures? I suspect you have some specific calculation in mind.
No calculation, but the fact is that mutations aren't usually "guided". They mostly occur randomly. That makes me wonder how such process could account for the origin of relevant functional information.

Just Bob · 10 February 2016

Wallace Barbosa de Souza said: No calculation, but the fact is that mutations aren't usually "guided". They mostly occur randomly. That makes me wonder how such process could account for the origin of relevant functional information.
Well, when most of the nonfunctional or dysfunctional information is pretty much self-eliminated from the gene pool, what you're left with will function well enough to work. Give us thousands of "stochastic" mutations, run them through the natural selection grinder, and what comes out is, by definition, functional.

Mike Elzinga · 10 February 2016

Wallace Barbosa de Souza said: No calculation, but the fact is that mutations aren't usually "guided". They mostly occur randomly. That makes me wonder how such process could account for the origin of relevant functional information.
Are you talking about "genetic entropy?" What is the physical barrier beyond which complex systems exhibiting complex behaviors are no longer possible? We know they exist; they are all around us. Why are they improbable if not impossible?

Henry J · 10 February 2016

Re "How do stochastic mutations are able to generate long strands with millions of correctly ordered nucleotides"

Mutations don't create "correctly ordered" anything. The combination of mutation and differential reproductive success (commonly called "natural selection") generates things that work. There is no "correct". There is "works well enough for now" and "doesn't work now".

Mike Elzinga · 10 February 2016

Wallace Barbosa de Souza said: That makes me wonder how such process could account for the origin of relevant functional information.
Another question: Just what is "relevant functional information?"

Just Bob · 12 February 2016

It was a drive-by IDioting.

All it took him was one good question to completely disprove evolution. No point in further discussion.

DS · 12 February 2016

Just Bob said: It was a drive-by IDioting. All it took him was one good question to completely disprove evolution. No point in further discussion.
Even though the answer was only two words (natural selection) and he hasn't addressed that? Well, I guess he can just declare victory and run away, just like every other creationist.

TomS · 12 February 2016

Wallace Barbosa de Souza said:
Mike Elzinga said:
Wallace Barbosa de Souza said: How do stochastic mutations are able to generate long strands with millions of correctly ordered nucleotides along with the inseparable proteic machinery that replicates, unzip, translate and repair the genome, not to mention the networks of several classes of RNAs and ncRNAs that play many crucial roles? Thank you in advance.
Just out of curiosity; could you explain what you mean by "stochastic mutations" and why you think atoms and molecules cannot evolve into complex structures? I suspect you have some specific calculation in mind.
No calculation, but the fact is that mutations aren't usually "guided". They mostly occur randomly. That makes me wonder how such process could account for the origin of relevant functional information.
I am not a scientist, so excuse my layman-type language. The adaptive immune system works by random variation plus selection. When the adaptive immune system detects an invader, it produces random variations of antibodies, and discards those which don't attack the invader. Eventually, there is produced a funtioning antibody. On the other hand, has anyone suggested any account for the appearance of functional information in the pattern shown in taxonomy, biogeography, etc., which does not include common descent with modification?

Henry J · 12 February 2016

On the other hand, has anyone suggested any account for the appearance of functional information in the pattern shown in taxonomy, biogeography, etc., which does not include common descent with modification?

POOF!!!111111!!!!eleven!!!

Wallace Barbosa de Souza · 16 February 2016

Mike Elzinga said: Are you talking about "genetic entropy?" What is the physical barrier beyond which complex systems exhibiting complex behaviors are no longer possible? We know they exist; they are all around us. Why are they improbable if not impossible?
No, I'm not talking about an upper limit to complexity. I'm just pondering about the claim that mutations can account for the origin and organization of every single biological feature, from basic components to entire hierarchically-organized molecular networks. Biomedical, genomic and system biology research are all showing countless results that follow when mutations occur, with many being very detrimental (fortunately, most mutations are "silenced" either by buffering or by any other intelligent mechanism present in the organisms that combat the dangerous results thereof), which puts the abovementioned claim at odds with current abundant evidence. How could mutations build these networks with thousands of genes, proteins, metabolites, TF's, epigenetic factors and all the other basic components that work together to convey emergent properties deemed essential to survival? Research keep showing over again that mutations, if anything, disrupt these orchestrated systems, which is a compelling sign of irreducibility.

Mike Elzinga · 16 February 2016

Wallace Barbosa de Souza said: How could mutations build these networks with thousands of genes, proteins, metabolites, TF's, epigenetic factors and all the other basic components that work together to convey emergent properties deemed essential to survival? Research keep showing over again that mutations, if anything, disrupt these orchestrated systems, which is a compelling sign of irreducibility.
Apparently you have never learned or understood the concept of natural selection. It is taught in good high school biology classes. Go look it up.

Mike Elzinga · 16 February 2016

Mike Elzinga said:
Wallace Barbosa de Souza said: How could mutations build these networks with thousands of genes, proteins, metabolites, TF's, epigenetic factors and all the other basic components that work together to convey emergent properties deemed essential to survival? Research keep showing over again that mutations, if anything, disrupt these orchestrated systems, which is a compelling sign of irreducibility.
Apparently you have never learned or understood the concept of natural selection. It is taught in good high school biology classes. Go look it up.
And, by the way, you should take time to learn about the chemistry and physics of biomolecules instead of just speculating on "reports" you have read but don't comprehend. Your "speculations" reveal you have no clue what you are talking about.

Wallace Barbosa de Souza · 16 February 2016

Mike Elzinga said:
Wallace Barbosa de Souza said: How could mutations build these networks with thousands of genes, proteins, metabolites, TF's, epigenetic factors and all the other basic components that work together to convey emergent properties deemed essential to survival? Research keep showing over again that mutations, if anything, disrupt these orchestrated systems, which is a compelling sign of irreducibility.
Apparently you have never learned or understood the concept of natural selection. It is taught in good high school biology classes. Go look it up.
Natural selection? You mean the tautological proposition that cannot make a single correct prediction? "And, by the way, you should take time to learn about the chemistry and physics of biomolecules" What do you think chemistry and physics can show in terms of biological networks and information?

Mike Elzinga · 16 February 2016

Wallace Barbosa de Souza said: What do you think chemistry and physics can show in terms of biological networks and information?
A hell of a lot more than you are aware. You need to go back to high school and start over.

Michael Fugate · 16 February 2016

Wallace Barbosa de Souza said: Natural selection? You mean the tautological proposition that cannot make a single correct prediction? "And, by the way, you should take time to learn about the chemistry and physics of biomolecules" What do you think chemistry and physics can show in terms of biological networks and information?
How is natural selection tautological? Please explain your reasoning.

Wallace Barbosa de Souza · 16 February 2016

Michael Fugate said: How is natural selection tautological? Please explain your reasoning.
That's a conclusion reached by many scientific thinkers like Karl Popper (curiously, the father of scientific falsifiability) Tam Hunt, who wrote: "Natural selection has been criticized as a tautology. This would be a major problem for evolutionary biology, if true, because tautological statements can't be falsified and, therefore, can't be scientific. There is merit to this critique insofar as the theory of natural selection is indeed generally described in a tautological manner. However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances." http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594354/ "A hell of a lot more than you are aware. You need to go back to high school and start over." What about presenting decent replies substantiated by data and scientific literature, instead of childish void words?

TomS · 16 February 2016

Wallace Barbosa de Souza said:
Michael Fugate said: How is natural selection tautological? Please explain your reasoning.
That's a conclusion reached by many scientific thinkers like Karl Popper (curiously, the father of scientific falsifiability) Tam Hunt, who wrote: "Natural selection has been criticized as a tautology. This would be a major problem for evolutionary biology, if true, because tautological statements can't be falsified and, therefore, can't be scientific. There is merit to this critique insofar as the theory of natural selection is indeed generally described in a tautological manner. However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances." http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594354/ "A hell of a lot more than you are aware. You need to go back to high school and start over." What about presenting decent replies substantiated by data and scientific literature, instead of childish void words?
http://ncse.com/cej/6/2/what-did-karl-popper-really-say-evolution What Did Karl Popper Really Say About Evolution by Frank J. Sonleitner Creation/Evolution, Issue 18 (Summer 1986)

Michael Fugate · 16 February 2016

Wallace Barbosa de Souza said:
Michael Fugate said: How is natural selection tautological? Please explain your reasoning.
That's a conclusion reached by many scientific thinkers like Karl Popper (curiously, the father of scientific falsifiability) Tam Hunt, who wrote: "Natural selection has been criticized as a tautology. This would be a major problem for evolutionary biology, if true, because tautological statements can't be falsified and, therefore, can't be scientific. There is merit to this critique insofar as the theory of natural selection is indeed generally described in a tautological manner. However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances." http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594354/ "A hell of a lot more than you are aware. You need to go back to high school and start over." What about presenting decent replies substantiated by data and scientific literature, instead of childish void words?
So you yourself don't understand if it is or isn't a tautology - you are only using hearsay that it might be? I asked for your reasoning, not someone else's. Lots of "ifs" in Hunt's statement.

Michael Fugate · 16 February 2016

Not to mention - I could find many, many philosophers - not to mention biologists - who say it isn't a tautology. Arguments from authority - meh...

Wallace Barbosa de Souza · 16 February 2016

Michael Fugate said:
Wallace Barbosa de Souza said:
Michael Fugate said: How is natural selection tautological? Please explain your reasoning.
That's a conclusion reached by many scientific thinkers like Karl Popper (curiously, the father of scientific falsifiability) Tam Hunt, who wrote: "Natural selection has been criticized as a tautology. This would be a major problem for evolutionary biology, if true, because tautological statements can't be falsified and, therefore, can't be scientific. There is merit to this critique insofar as the theory of natural selection is indeed generally described in a tautological manner. However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances." http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594354/ "A hell of a lot more than you are aware. You need to go back to high school and start over." What about presenting decent replies substantiated by data and scientific literature, instead of childish void words?
So you yourself don't understand if it is or isn't a tautology - you are only using hearsay that it might be? I asked for your reasoning, not someone else's. Lots of "ifs" in Hunt's statement.
So, are you telling me that you DO understand natural selection? Then hurry and go tell the scientists, because they have no idea. Still awaiting explanations about mutations bringing about biological systems.

Wallace Barbosa de Souza · 16 February 2016

TomS said:
Wallace Barbosa de Souza said:
Michael Fugate said: How is natural selection tautological? Please explain your reasoning.
That's a conclusion reached by many scientific thinkers like Karl Popper (curiously, the father of scientific falsifiability) Tam Hunt, who wrote: "Natural selection has been criticized as a tautology. This would be a major problem for evolutionary biology, if true, because tautological statements can't be falsified and, therefore, can't be scientific. There is merit to this critique insofar as the theory of natural selection is indeed generally described in a tautological manner. However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances." http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594354/ "A hell of a lot more than you are aware. You need to go back to high school and start over." What about presenting decent replies substantiated by data and scientific literature, instead of childish void words?
http://ncse.com/cej/6/2/what-did-karl-popper-really-say-evolution What Did Karl Popper Really Say About Evolution by Frank J. Sonleitner Creation/Evolution, Issue 18 (Summer 1986)
"Early in his career, the philosopher Karl Popper (yes, cited by F and P-P) called evolution via natural selection "almost a tautology" and "not a testable scientific theory but a metaphysical research program." Attacked for these criticisms, Popper took them back. But when I interviewed him in 1992, he blurted out that he still found Darwin's theory dissatisfying. "One ought to look for alternatives!" Popper exclaimed, banging his kitchen table." http://blogs.scientificamerican.com/cross-check/dubitable-darwin-why-some-smart-nonreligious-people-doubt-the-theory-of-evolution/

Michael Fugate · 16 February 2016

Can't answer a simple question Wallace? - thought not.

Notice how your body Tam, says that it is possible to predict outcomes. So of course it is not a tautology.
You are not even smart enough to read your own citation.

Michael Fugate · 16 February 2016

buddy - not body - damn spellcheck.....

Wallace Barbosa de Souza · 16 February 2016

Michael Fugate said: Can't answer a simple question Wallace? - thought not. Notice how your body Tam, says that it is possible to predict outcomes. So of course it is not a tautology. You are not even smart enough to read your own citation.
He's saying clearly that when natural selection has its tautology undone, it showss its lack of predictability. In order to "predict" and "explain" away anything in biology, NS needs to receive tons of "patchs", adjusts, ad hoc exceptions, in short, it need to turn into a tautology, because it cannot predict a thing.

Michael Fugate · 16 February 2016

You can't read Wallace. Period.
However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances.
Clearly he is saying it can make testable predictions and they have borne out. He is also saying that if we knew more, then we could make better prediction and be able to test those too. May be you need to start over with reading comprehension before embarking on chemistry and physics.

DS · 16 February 2016

Wallace Barbosa de Souza said:
Michael Fugate said: Can't answer a simple question Wallace? - thought not. Notice how your body Tam, says that it is possible to predict outcomes. So of course it is not a tautology. You are not even smart enough to read your own citation.
He's saying clearly that when natural selection has its tautology undone, it showss its lack of predictability. In order to "predict" and "explain" away anything in biology, NS needs to receive tons of "patchs", adjusts, ad hoc exceptions, in short, it need to turn into a tautology, because it cannot predict a thing.
Sorry, no. Natural selection makes very precise predictions. What exactly do you think all those equations are for? If you don't understand how it works, here is a video to help clarify: https://www.youtube.com/watch?v=sjeSEngKGrg We can predict exactly what the outcome of selection will be in each of the environments. We can predict how long it will take for the changes to occur. And we can predict what the outcome will be if the environment changes again. Exactly how is this not prediction? Exactly what is your problem?

Mike Elzinga · 16 February 2016

Wallace Barbosa de Souza said: What about presenting decent replies substantiated by data and scientific literature, instead of childish void words?
It's easier to present a reply to a real question rather than to a ignorant assertion that reveals an unwillingness to dig into the scientific concepts themselves. I asked you earlier what barriers you think prevent atoms and molecules from forming complex systems that have complex properties and behaviors. Why do you think they can't when we can see that they clearly exist all around us? Instead of trying to jump to "philosophical" arguments before you understand scientific concepts, try learning the scientific concepts and some scientific facts first. Take a look at the work of the people who won the 2013 Nobel Prize in chemistry; you might just get a hint that scientists know considerably more about complex molecular systems than you do.

TomS · 16 February 2016

Wallace Barbosa de Souza said:
TomS said:
Wallace Barbosa de Souza said:
Michael Fugate said: How is natural selection tautological? Please explain your reasoning.
That's a conclusion reached by many scientific thinkers like Karl Popper (curiously, the father of scientific falsifiability) Tam Hunt, who wrote: "Natural selection has been criticized as a tautology. This would be a major problem for evolutionary biology, if true, because tautological statements can't be falsified and, therefore, can't be scientific. There is merit to this critique insofar as the theory of natural selection is indeed generally described in a tautological manner. However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances." http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594354/ "A hell of a lot more than you are aware. You need to go back to high school and start over." What about presenting decent replies substantiated by data and scientific literature, instead of childish void words?
http://ncse.com/cej/6/2/what-did-karl-popper-really-say-evolution What Did Karl Popper Really Say About Evolution by Frank J. Sonleitner Creation/Evolution, Issue 18 (Summer 1986)
"Early in his career, the philosopher Karl Popper (yes, cited by F and P-P) called evolution via natural selection "almost a tautology" and "not a testable scientific theory but a metaphysical research program." Attacked for these criticisms, Popper took them back. But when I interviewed him in 1992, he blurted out that he still found Darwin's theory dissatisfying. "One ought to look for alternatives!" Popper exclaimed, banging his kitchen table." http://blogs.scientificamerican.com/cross-check/dubitable-darwin-why-some-smart-nonreligious-people-doubt-the-theory-of-evolution/
Is natural selection a tautology and therefore not science? What is the topic?

Mike Elzinga · 16 February 2016

Wallace Barbosa de Souza said: So, are you telling me that you DO understand natural selection? Then hurry and go tell the scientists, because they have no idea. Still awaiting explanations about mutations bringing about biological systems.
Tell us how a system of atoms and molecules that cannot "mutate" can explore different configurations and be subjected to selection. Atomic and molecular assemblies that are so tightly bound that they can't change don't mutate; they stay the way they are? Mutations are a necessary part of the building of complex systems and of exploring a wide range of properties and behaviors. Soft matter changes and evolves; and it becomes subject to natural selection. Rigid systems don't change; and the atoms and molecules in gases aren't sufficiently bound together to form any kind of system that persists long enough to provide a template for another level of development. Gaseous systems come all apart nearly instantly. Don't confuse the various phases of matter. Students learn about these concepts in middle school.

Michael Fugate · 16 February 2016

If creationists had any understanding of science or history, they would, of course, no longer be creationists -it's the ignorance that keeps them in the fold. The whole concept of fixity, of unchangeability, of non-mutability, is a post-Darwinian creation. Variation and selection drove agriculture. When creationists admit this, then it is the "micro-macro mambo", as SC puts it, that comes into play. As Mike points out for chemical systems, there aren't universal barriers to change in biological systems either. Speciation happens - easily witnessed. Genetic continuity happens - easily witnessed.

Give up ignorance for Lent, Wallace - it will do you good.

DS · 16 February 2016

"One ought to look for alternatives!" Popper exclaimed, banging his kitchen table." http://blogs.scientificamerican.com/cross-check/dubitable-darwin-why-some-smart-nonreligious-people-doubt-the-theory-of-evolution/

Sure. Found any yet? Didn't think so.

TomS · 16 February 2016

DS said: "One ought to look for alternatives!" Popper exclaimed, banging his kitchen table." http://blogs.scientificamerican.com/cross-check/dubitable-darwin-why-some-smart-nonreligious-people-doubt-the-theory-of-evolution/ Sure. Found any yet? Didn't think so.
Sexual selection. Genetic drift. Is there anyone (other than creationists) who would not accept the search for alternatives?

Wallace Barbosa de Souza · 16 February 2016

Michael Fugate said: You can't read Wallace. Period.
However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances.
Clearly he is saying it can make testable predictions and they have borne out. He is also saying that if we knew more, then we could make better prediction and be able to test those too. May be you need to start over with reading comprehension before embarking on chemistry and physics.
"However, natural selection can be described non-tautologically if we’re careful." That makes no sense. 160 years since evolution has been presented to the world and still its proponents haven't been "careful" enough to formulate a model that can make predictions? That "careful" talk just seems more of the usual tautological adjust that evolution has undergone countless times in the last century and half, because a huge load of data came up that simply did not fit the original framework of NS. In the meantime, theory of relativity didn't need any additional adjust ever since Einstein's time. And it has made contribution upon contribution to its field. "May be you need to start over with reading comprehension before embarking on chemistry and physics." It's obvious that tme will pass indefinitely and you won't come up with any insight from these fields at all.

Michael Fugate · 16 February 2016

Face Palm! Now you are disagreeing with your own example? You were the one that cited Hunt in the first place. So you think that all change has to be due to NS, really? You can't be that dumb, can you?

Mike Elzinga · 16 February 2016

Wallace Barbosa de Souza said:
Michael Fugate said: You can't read Wallace. Period.
However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances.
Clearly he is saying it can make testable predictions and they have borne out. He is also saying that if we knew more, then we could make better prediction and be able to test those too. May be you need to start over with reading comprehension before embarking on chemistry and physics.
"However, natural selection can be described non-tautologically if we’re careful." That makes no sense. 160 years since evolution has been presented to the world and still its proponents haven't been "careful" enough to formulate a model that can make predictions? That "careful" talk just seems more of the usual tautological adjust that evolution has undergone countless times in the last century and half, because a huge load of data came up that simply did not fit the original framework of NS. In the meantime, theory of relativity didn't need any additional adjust ever since Einstein's time. And it has made contribution upon contribution to its field. "May be you need to start over with reading comprehension before embarking on chemistry and physics." It's obvious that tme will pass indefinitely and you won't come up with any insight from these fields at all.
Is this character a poe? Apparently this character thinks that natural selection is supposed to make precise mathematical predictions like Newtonian mechanics or Einstein's relativity. This appears to be consistent with the general science and math illiteracy among ID/creationists. It is not possible to explain even the most basic scientific concepts to a follower of ID/creationism. Most can't do basic algebra. Throw in stochastic processes in the presence of powerful forces that set the boundary conditions on what can happen; well, that is just too confusing for someone who can't keep track of more than one thing.

DS · 16 February 2016

Wallace Barbosa de Souza said:
Michael Fugate said: You can't read Wallace. Period.
However, natural selection can be described non-tautologically if we’re careful. Natural selection should be defined as the theory that attempts to predict and retrodict evolutionary change through environmental forces acting upon organisms. However, this re-framing comes at a cost: it reveals, based on our current knowledge of evolutionary forces, the lack of ability to make accurate predictions about expected changes except in the most simple of circumstances.
Clearly he is saying it can make testable predictions and they have borne out. He is also saying that if we knew more, then we could make better prediction and be able to test those too. May be you need to start over with reading comprehension before embarking on chemistry and physics.
"However, natural selection can be described non-tautologically if we’re careful." That makes no sense. 160 years since evolution has been presented to the world and still its proponents haven't been "careful" enough to formulate a model that can make predictions? That "careful" talk just seems more of the usual tautological adjust that evolution has undergone countless times in the last century and half, because a huge load of data came up that simply did not fit the original framework of NS. In the meantime, theory of relativity didn't need any additional adjust ever since Einstein's time. And it has made contribution upon contribution to its field. "May be you need to start over with reading comprehension before embarking on chemistry and physics." It's obvious that tme will pass indefinitely and you won't come up with any insight from these fields at all.
Seriously dude, you need to become more educated. Perhaps you can tell us the PREDICTION that would be made regarding allele frequencies in the case of heterozygote superiority. What is the PREDICTED equilibrium allele frequency given the relative fitness values of 0.20 and 0.80 for the homozygous recessive and homozygous dominant, respectively. Until you can answer this question, you have no business criticizing what you obviously don't understand. When you can answer this question, you will realize how ridiculous your reasoning is and you will stop saying such ignorant things.

Mike Elzinga · 16 February 2016

DS said: Until you can answer this question, you have no business criticizing what you obviously don't understand. When you can answer this question, you will realize how ridiculous your reasoning is and you will stop saying such ignorant things.
All I can do is just shake my head at such lunk-headedness Frequencies, distributions, means, standard deviations, large numbers, the Central Limit Theorem, emergent patterns in the limits of large numbers, the laws of chemistry and physics, statistical mechanics and thermodynamics; these all seem to be far above the heads of people who are brought up in the culture of sectarian objections to evolution. But so is just about every other major concept in science and mathematics. Everything in evolution is a tornado-in-a- junkyard scenario to them. There are no forces or interactions among atoms and molecules; they can be represented by ASCII characters or dice or coin flips. Calculating probabilities is merely a matter of asserting 1/KN. If you take logarithms to base 2 and call it "information," this becomes really, really, really advanced math in ID/creationist land; so advanced that scientists have never understood it. Oh; and "philosophy" trumps science.

Just Bob · 16 February 2016

And we must ignore all the advances and daily practical progress science has made and constantly makes using those concepts and theories that (for philosophical reasons) can't possibly be true.

Just Bob · 16 February 2016

So Wallace, what's your solution? Magic?

Performed by whom?

When?

And wait for it... it's coming... it's almost here! Here it is: Can you name something that is NOT 'designed'? If you can, please explain how you know it isn't 'designed'. Better yet (and more scientifically) explain how to objectively TEST whether something is designed or not.

DS · 17 February 2016

Well Wallace, still waiting. Watched that video yet? Still think that natural selection makes no predictions? Still think that mutations cannot provide the raw material for adaptation? Did you notice that the color change occurred independently in different populations due to different mutations? Perhaps you have some alternative explanation?

You do know that the equations for natural selection accurately predicted the frequency of the sickle cell anemia allele in malaria infested areas don't you? I can provide you with a reference from the scientific literature if you like, but I have found that creationists view the literature the same way that vampires view holy water, to be avoided at all costs.

Just Bob · 17 February 2016

Just Bob said: Can you name something that is NOT 'designed'? If you can, please explain how you know it isn't 'designed'. Better yet (and more scientifically) explain how to objectively TEST whether something is designed or not.
Why is it that they can never, as far as I've seen, answer such simple questions about the premises at the very foundation of their belief system? I give Wallace about a 30% likelihood of even trying.

Michael Fugate · 17 February 2016

I am sure Wallace visited one of the creationist sites with "15 questions that evolutionists can't answer". He picked "natural selection is a tautology and makes no predictions" and trotted on over. He doesn't have the background to make any sense of any of our replies or queries. He probably thinks tautology is the study of young children.

Just Bob · 17 February 2016

Michael Fugate said: He probably thinks tautology is the study of young children.
Everybody know it's the study of knots.

Michael Fugate · 17 February 2016

Unless it is tatertautology, then it the study of something quite different.
Just Bob said:
Michael Fugate said: He probably thinks tautology is the study of young children.
Everybody know it's the study of knots.
Unless it is tatertautology, then it is the study of fast food.

TomS · 17 February 2016

Michael Fugate said: I am sure Wallace visited one of the creationist sites with "15 questions that evolutionists can't answer". He picked "natural selection is a tautology and makes no predictions" and trotted on over. He doesn't have the background to make any sense of any of our replies or queries. He probably thinks tautology is the study of young children.
I recall reading long ago the idea that F=ma is a tautology. The point being that force and mass are defined by and measured by that equation.

Henry J · 17 February 2016

I recall reading long ago the idea that F=ma is a tautology. The point being that force and mass are defined by and measured by that equation.

Maybe, but that's only when there's only one force. It's only net force that = ma. (Or was that a Freudian slip?)

Mike Elzinga · 17 February 2016

TomS said:
Michael Fugate said: I am sure Wallace visited one of the creationist sites with "15 questions that evolutionists can't answer". He picked "natural selection is a tautology and makes no predictions" and trotted on over. He doesn't have the background to make any sense of any of our replies or queries. He probably thinks tautology is the study of young children.
I recall reading long ago the idea that F=ma is a tautology. The point being that force and mass are defined by and measured by that equation.
The reason that it is not a tautology is because each of F, m, and a can be defined operationally and independently using various methods. Once each has been defined, one can discover experimentally that F = ma is true. For example, F can be defined as being proportional to the amount of extension or compression of a spring. The mass can be expressed in multiples of some arbitrary size of a piece of lead. You could use units of "lumps" if you like. Distance can be measured in multiples of some standard length such as the distance from elbow to middle fingertip. Time can be measured by the amount of water that has dripped from a reservoir into a container below; or by the number of beats of a heart. All of these various "units" would eventually produce the conclusion that units of spring extension is proportional to lumps times the change in speed (distance per drip) per drip. Probably one of the reasons it took so long to recognize that F = ma (it wasn't until Newton made it explicit) was because doing the experiment of measuring time and distance accurately was difficult with crude units; but more importantly because people didn't recognize in the presence of ubiquitous friction. They didn't understand that the experiment had to be done with unbalanced forces over and above friction and that pushing on something under those conditions made things go faster and faster. Even today it is hard to get students to push or pull a mass using a spring kept at constant compression or extension. When they do such an experiment, they discover that they have to continuously speed up in order to keep the spring at a constant length. Of course, with linear air tracks that nearly eliminate friction, and with a weight hung over a pulley to produce a constant force, it requires some pretty accurate timers and time markers to produce a good graph from which one can discover the relationship. The reason that F = ma is not a tautology is because it could have been otherwise - and, in fact, was thought to be otherwise for centuries. If we were like bacteria or other small organisms swimming in a viscous medium, we would have discovered that speed, not acceleration, was proportional to force. In an even more viscous medium we would conclude that distance was proportional to force.

Michael Fugate · 18 February 2016

Where's Waldo?

Just Bob · 19 February 2016

Michael Fugate said: Where's Waldo?
Since he's, like, totally disproved evolution, dude, he doesn't need to hang around anymore.

stevaroni · 19 February 2016

Mike Elzinga said: The mass can be expressed in multiples of some arbitrary size of a piece of lead. You could use units of "lumps" if you like.
Isn't one of the old imperial standards of mass the "slug" or something like that? I pretty much put that one out of my head, I eventually got so sick of all the weird imperial constants I long ago started religiously to convert everything to SI units, do the problem, the convert back rather than constantly tracking how many ounce-inches go into a foot-pound. With Si units the only weird conversion is 9.8 newtons to a kilogram. Even the speed of light is a round number at 300,000Km/s.

fnxtr · 19 February 2016

So I guess Ohm's Law is a tautology, too. :-/

juegos 2 · 20 February 2016

Thank your article. very helpful article. thank you very much. :)

Mike Elzinga · 20 February 2016

fnxtr said: So I guess Ohm's Law is a tautology, too. :-/
Only when recited while sitting in the lotus position.

TomS · 20 February 2016

fnxtr said: So I guess Ohm's Law is a tautology, too. :-/
I don't know what creationists who cite Popper have to say about Newton's and Ohm's laws, etc.

Just Bob · 20 February 2016

TomS said:
fnxtr said: So I guess Ohm's Law is a tautology, too. :-/
I don't know what creationists who cite Popper have to say about Newton's and Ohm's laws, etc.
They'll say whatever proves evolution is impossible. And in their fantasy physics, that's everything because, you know, evolution CAN'T be true. So they'll find something in any law of physics to prove what they know has to be true because [insert Bible verse here].

TomS · 20 February 2016

Just Bob said:
TomS said:
fnxtr said: So I guess Ohm's Law is a tautology, too. :-/
I don't know what creationists who cite Popper have to say about Newton's and Ohm's laws, etc.
They'll say whatever proves evolution is impossible. And in their fantasy physics, that's everything because, you know, evolution CAN'T be true. So they'll find something in any law of physics to prove what they know has to be true because [insert Bible verse here].
That makes me wonder about The Law of Conservation of Designeroid Information, or the Laws of Creationist Thermodynamics, or the Universal Probability Bound. Are they tautologies?

stevaroni · 20 February 2016

TomS said: That makes me wonder about The Law of Conservation of Designeroid Information, or the Laws of Creationist Thermodynamics, or the Universal Probability Bound. Are they tautologies?
Obviously, they're proponetists of all things Cdesign.

Wallace Barbosa de Souza · 1 March 2016

Wow, back here after a month and still haven't seen a decent, mature reply by evolution supporters.. Ad hominem, group mockery, more ad hominem and irrelevant talk, and no solid argument to support Darwinian tautology!

The real predictive nature of evolution is better understood in the words of Philip Skell, who wrote:

"Further, Darwinian explanations for such things are often too supple: Natural selection makes humans self-centered and aggressive – except when it makes them altruistic and peaceable. Or natural selection produces virile men who eagerly spread their seed – except when it prefers men who are faithful protectors and providers. When an explanation is so supple that it can explain any behavior, it is difficult to test it experimentally, much less use it as a catalyst for scientific discovery." (The Scientist 2006)

Is this laughable pseudoscience that you guys are trying to tout as the basis of biology? LOL

Change in alleles.. Change in alleles.... An old conception held by minds that lived a century ago, certainly that babbling explains the origin and organization of "modern" organisms, the complexity of which defies reason..

How does changes in allele frequencies explain the origin of large metabolic pathways, PPI modules and networks, orchestrated behavior of gene cascades, cell compartmentalisation, differentiation, molecular complexes like spliceosomes, organs like hearts and brains, etc.. How in the world does that old conjecture explain the evolution of these things AT MOLECULAR LEVEL?

That's the challenge, I'll only reply decent replies by actual adults.. Kids are gonna be utterly ignored

phhht · 1 March 2016

Change in alleles.. Change in alleles.… An old conception held by minds that lived a century ago, certainly that babbling explains the origin and organization of “modern” organisms, the complexity of which defies reason..

Mass-energy equivalence... Mass-energy equivalence ... An old conception held by minds that lived a century ago, certainly that babbling explains the origin and organization of “modern” nuclear bombs, the complexity of which defies reason...

Wallace Barbosa de Souza · 1 March 2016

Just Bob said:
"So Wallace, what's your solution? Magic?"
Nope, intelligent design. Magic is a term that better fits the idea tha random mutations generate circulatory systems and stem cell regulatory networks.
"Performed by whom?"
Childish question, anyway, ID science doesn't advocate any particular kind of designer, we only point out the obvious, that is, the fact that life is designed.
"When?"
Sorry but I don't know (and I won't make up chronological timelines like Darwinians do), and it's irrelevant to evaluate the detection of design.
"And wait for it... it's coming... it's almost here! Here it is: Can you name something that is NOT 'designed'? If you can, please explain how you know it isn't 'designed'. Better yet (and more scientifically) explain how to objectively TEST whether something is designed or not."
Ah, finally a decent question! To summarize, life is designed because it has all the signs of designed/engineered complex systems, including: -Information storage, processing and flow; -Emergent properties responsible for every function; -Organized non-random structures including intelligent compartmentalisation; -Modulation of molecules; -Networks and cascades of finely regulated molecules (genes, proteins, enzymes, transcription factors, epigenetic factors, microRNAs, etc), strongly resembling internet network. The very present of motors like ATPase and flagellum are sufficient evidence for ID.

Mike Elzinga · 1 March 2016

Wallace Barbosa de Souza said: Wow, back here after a month and still haven't seen a decent, mature reply by evolution supporters...
Wow; in a month most students can learn several important concepts in science. Several such concepts have been presented on this very thread, but you apparently didn't notice. Why is that? Just trolling are you?

Mike Elzinga · 1 March 2016

Wallace Barbosa de Souza said: -Information storage, processing and flow; -Emergent properties responsible for every function; -Organized non-random structures including intelligent compartmentalisation; -Modulation of molecules; -Networks and cascades of finely regulated molecules (genes, proteins, enzymes, transcription factors, epigenetic factors, microRNAs, etc), strongly resembling internet network. The very present of motors like ATPase and flagellum are sufficient evidence for ID.
What happens to those "motors" and "functions" when the temperature drops below about 60 degrees Fahrenheit? Can you explain what happens and why? I suspect you don't have a clue about the significance of temperature dependence. I predict that all you can supply is a silly response that has nothing to do with anything.

phhht · 1 March 2016

Wallace Barbosa de Souza said: Just Bob said:
"So Wallace, what's your solution? Magic?"
Nope, intelligent design. Magic is a term that better fits the idea tha random mutations generate circulatory systems and stem cell regulatory networks.
"Performed by whom?"
Childish question, anyway, ID science doesn't advocate any particular kind of designer, we only point out the obvious, that is, the fact that life is designed.
"When?"
Sorry but I don't know (and I won't make up chronological timelines like Darwinians do), and it's irrelevant to evaluate the detection of design.
"And wait for it... it's coming... it's almost here! Here it is: Can you name something that is NOT 'designed'? If you can, please explain how you know it isn't 'designed'. Better yet (and more scientifically) explain how to objectively TEST whether something is designed or not."
Ah, finally a decent question! To summarize, life is designed because it has all the signs of designed/engineered complex systems, including: -Information storage, processing and flow; -Emergent properties responsible for every function; -Organized non-random structures including intelligent compartmentalisation; -Modulation of molecules; -Networks and cascades of finely regulated molecules (genes, proteins, enzymes, transcription factors, epigenetic factors, microRNAs, etc), strongly resembling internet network. The very present of motors like ATPase and flagellum are sufficient evidence for ID.
What horseshit. ID IS magic. It depends on the presupposed existence of a magical designer, one that works by unknown means, through unknown pathways, and with completely mysterious and unnecessary motivations and powers. One postulates the action of a divine actor in a simple-minded pseudoscientific parody of rationality. It's classically unsupported pseudoscience: no clear definitions, no testable evidence, no experiment, nothing at all but denial, incredulity, baseless claims and unsupported assertions. All the IDiots have is insistence that they are right in their so-called inferences. Not a single one of Barby's "signs" amounts to anything other than a god-of-the-gaps argument, allegedly of worth because... well, because Barby says so. Nothing more. You can see this clearly when he claims that "The very present [sic] of motors like ATPase and flagellum are sufficient evidence for ID." There is no reason whatsoever to suppose that ATPase and flagella did not evolve, much less that they were created ex nihilo by some purported supernatural engineer.

DS · 1 March 2016

Wallace Barbosa de Souza said: Wow, back here after a month and still haven't seen a decent, mature reply by evolution supporters.. Ad hominem, group mockery, more ad hominem and irrelevant talk, and no solid argument to support Darwinian tautology! The real predictive nature of evolution is better understood in the words of Philip Skell, who wrote: "Further, Darwinian explanations for such things are often too supple: Natural selection makes humans self-centered and aggressive – except when it makes them altruistic and peaceable. Or natural selection produces virile men who eagerly spread their seed – except when it prefers men who are faithful protectors and providers. When an explanation is so supple that it can explain any behavior, it is difficult to test it experimentally, much less use it as a catalyst for scientific discovery." (The Scientist 2006) Is this laughable pseudoscience that you guys are trying to tout as the basis of biology? LOL Change in alleles.. Change in alleles.... An old conception held by minds that lived a century ago, certainly that babbling explains the origin and organization of "modern" organisms, the complexity of which defies reason.. How does changes in allele frequencies explain the origin of large metabolic pathways, PPI modules and networks, orchestrated behavior of gene cascades, cell compartmentalisation, differentiation, molecular complexes like spliceosomes, organs like hearts and brains, etc.. How in the world does that old conjecture explain the evolution of these things AT MOLECULAR LEVEL? That's the challenge, I'll only reply decent replies by actual adults.. Kids are gonna be utterly ignored
Really? So you answered my questions about selection? No? Then stop with the crocodile tears already. You get treated the way you deserve around here.

DS · 1 March 2016

Funny you should bring up spliceosomes. Here is a recent article on spliceosome evolution:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2650416/

As usual, gene duplication, mutation and natural selection played major roles in the evolution of modern spliceosomes. This is how things evolve at the MOLECULAR LEVEL. If you want to claim that they could not have evolved, you are going to have to deal with the evidence that they in fact did just that. Incredulity is not an argument.

DS · 2 March 2016

Still waiting cream puff. You still haven't answered my questions about natural selection. If you had, you would realize that you were totally and completely wrong when you claimed that it made no predictions. And we know a great deal about evolution at the molecular level. Apparently you are not familiar with the scientific literature. Are you just a kid, coming here to shoot spit wads at the grownups? You can't handle the evidence. When you are ready to confront reality, let us know.

DS · 2 March 2016

While we are waiting for your response, her is an article about the evolution of the heart from bacteria to man:

http://onlinelibrary.wiley.com/doi/10.1196/annals.1341.002/abstract

DS · 2 March 2016

And while we are at it, here is a review article on vertebrate brain evolution:

http://icb.oxfordjournals.org/content/42/4/743.full

Michael Fugate · 2 March 2016

Wallace, it took you a whole month to find a list of creationist clichés? I am sure I could have found them in 30 minutes or less.

So is natural selection still a tautology, or have you given up on that particular argument? Can you list all the different ways a mutation can arise? Can you list all the ways a protein can be influenced by it primary, secondary and tertiary sequences, by the internal environment, by the external environment?

Is everything designed? or only some things? I can find an organized structural pattern in a rock or in soil, are they designed? Water has emergent properties, is it designed? I can find information in anything with a pattern.

Who do you think the "designer" is? What do you base that on? Given who the designer is how might that influence what it does? Would different designers do things differently?