At UD I noticed, while I was checking the Moran-Arrington score, I couldn’t help noticing a news item entitled, provocatively (for me) Psychology does not speak the language of statistics very well.
So being a psychologist who teaches statistical methods to psychology students, I had to click, and found that it was a report of a blog piece here called Statistics Shows Psychology Is Not Science
There’s been a skirmish between Larry Moran and Barry Arrington about whether Barry understands the Theory of Evolution, and the latest salvo is a piece at UD, entitled, Can a Lowly Lawyer Make a Useful Contribution? Maybe.
Well, in a sense, Barry makes a useful contribution in that post, as he gives a very nice illustration of a common misunderstanding about the process of hypothesis testing, in this case, basic model-fitting and null hypothesis testing, the workhorse (with all its faults) of scientific research. Barry writes:
[Philip]Johnson is saying that attorneys are trained to detect baloney. And that training is very helpful in the evolution debate, because that debate is chock-full of faulty logic (especially circular reasoning), abuse of language (especially equivocations), assumptions masquerading as facts, unexamined premises, etc. etc.
Consider, to take one example of many, cladistics. It does not take a genius to know that cladistic techniques do not establish common descent; rather they assume it. But I bet if one asked, 9 out of 10 materialist evolutionists, even the trained scientists among them, would tell you that cladistics is powerful evidence for common descent. As Johnson argues, a lawyer’s training may help him understand when faulty arguments are being made, sometimes even better than those with a far superior grasp of the technical aspects of the field. This is not to say that common descent is necessarily false; only cladistics does not establish the matter one way or the other.
In summary, I am trained to evaluate arguments by stripping them down to examine the meaning of the terms used, exposing the underlying assumptions, and following the logic (or, as is often the case, exposing the lack of logic). And I think I do a pretty fair job of that, both in my legal practice and here at UD.
Barry has made two common errors here. First he has confused the assumption of common descent with the conclusion of common descent, and thus detected circular reasoning where there is none. Secondly he has confused the process of fitting a model with the broader concept of a hypothesised model.
As Tom English’s post critiquing Dembski, Ewert, Marks, (eg Ewert) is being swamped with OT stuff, I offer this as a place to discuss the lack of substantive responses to Tom English and Joe Felsenstein so that any substantive response to Tom’s points will be more visible.
About a year ago, Joe Felsenstein critiqued a seminar presentation by William Dembski, “Conservation of Information in Evolutionary Search.” He subsequently discussed Dembski’s primary source with me, and devised a brilliant response, unlike any that I had considered. This led to an article, due mostly to Felsenstein, though I contributed, at The Panda’s Thumb. Nine days after it appeared, Dembski was asked in a radio interview whether anyone was paying attention to his technical work. Surely a recipient of
qualifies as a someone. But Dembski changed the topic. And when the question came around again, he again changed the topic. Mind you, this isn’t how I know that Felsenstein blasted conservation of “information,” which is not information, in evolutionary “search,” which does not search. It’s how I know that Dembski knows.
Lamarckism (or Lamarckian inheritance) is the idea that an organism can pass on characteristics that it acquired during its lifetime to its offspring (also known as heritability of acquired characteristics or soft inheritance).
– Wikipedia
Many of us have probably been taught that Lamarkian inheritance is anathema. Heresy. But why would that be the case? Is it for theoretical reasons or simply because of a lack of empirical evidence?
At Uncommon Descent, a News posting by Denyse O’Leary shows us a video by Jonathan McLatchie. News then expects “Darwin faithful” to “create a distraction below”.
McLatchie defines Specified Complexity as information that matches a predefined pattern, such as specific protein folds needed to have a particular function. His video is in a series entitled “One Minute Apologist” (he takes 2 minutes).
He never says anything to clarify whether natural selection can put this information into the genome. We’ve discussed these points many times before, but let me briefly mention the dilemma that he doesn’t resolve for us:
1, Complex Specified Information was defined by William Dembski in No Free Lunch in this way. The high level of improbability that he required was supposed to show that random mutation could not produce CSI. And a Law of Conservation of Complex Specified Information was supposed to show that natural selection could not achieve CSI. Unfortunately the LCCSI is not formulated so as to be able to do that, because it changes the specification in the before and after states.
2. So in 2005-2006 Dembski instead defined Specified Complexity. Now it is a measure of how improbably far out we are on the scale of specification, with the improbability defined this time as computed taking not only mutation into account, but also natural selection. Dembski does not say how to compute that probability. Now SC really does rule out natural selection — simply by being defined so as to do so. It thereby becomes a useless add-on quantity, computable only once one has already found some other way to show that the information cannot be put into the genome by natural selection.
McLatchie presumably wants to clear us all up on this, but he seems to be using the definition of 1 with the name of 2. So we end up confused as to whether his quantity can be put into the genome by natural selection, or whether it is a useless after-the-fact add-on to some other argument which establishes that it can’t. And he’s had a whole extra minute.
http://www.dailymail.co.uk/embed/video/1226759.html
Are you excited, non materialists?
My precognition says, “fake”
Wesley Elsberry reminds us that the tenth anniversary of the Kitzmiller vs. Dover Area School District is fast approaching. In his inimitable low-key but hard-hitting style, he writes: Continue reading
I recently came across this book:
Biosemiotics: Information, Codes and Signs in Living Systems
This new book presents contexts and associations of the semiotic view in biology, by making a short review of the history of the trends and ideas of biosemiotics, or semiotic biology, in parallel with theoretical biology. Biosemiotics can be defined as the science of signs in living systems. A principal and distinctive characteristic of semiotic biology lies in the understanding that in living, entities do not interact like mechanical bodies, but rather as messages, the pieces of text. This means that the whole determinism is of another type.
Pardon my skepticism, but
Biosemiotics is the study of things that just don’t exist. Theology for biologists.
The Hiddenness of God
The famous mathematician and atheist, Bertrand Russell (co-founder of analytic philosophy), was asked about what he would say if he had to stand before God one day to give account for his unbelief. His answer:
“Sir, why did you take such pains to hide yourself?”
Upright Biped has announced the launch of his site via this UD post: Writing Biosemiosis-org
All of the unique physical conditions of dimensional semiosis have already been observed and documented in the scientific literature. It is an intractable fact that a dimensional semiotic system is used to encode organic polymers inside the cell. The conclusion of intelligent action is therefore fully supported by the physical evidence, and is subject to falsification only by showing an unguided source capable of creating such a system.
http://biosemiosis.org/index.php/a-scientific-hypothesis-of-design
Discuss!
My intent here in these recent posts on the genetic code has been to expose the absurdity of Code Denialism. The intent has not been to make the case for intelligent design based upon the existence of biological codes. I know some people find that disconcerting but that would be putting the cart before the horse. No one is going to accept a conclusion when they deny the premise. And please forgive me if I choose not to play the game of “let’s pretend it really is a code” while you continue to deny that it actually is a code.
First I’d like to thank you. It’s actually been pretty neat looking up and reading many of these resources in my attempt to see whether I could defend the thesis that the genetic code is a real code. I admit it’s also been much too much fun digging up all the reasons why code denialism is just plain silly (and irrational).
That the genetic code is a code is common usage and if “meaning is use” that alone ought to settle the matter. But this is “The Skeptical Zone” and Code Denialism is strong here. But I’m not just claiming that it’s a code because we say it’s a code in common usage. I’m claiming it is a code because it meets the definition of a code. The reason we say it is a code is because it is in fact a code.
My first two posts have been on some of the major players and how they understood they were dealing with a code and how that guided their research. I’ll have more to say on that in the future as it’s a fascinating story. But for now …
What A Code Is
Here’s a great presentation on the new colourmaps in python for all you coders / devs (We’re using them now). For non-coders some insights into perception, evolution of colour vision and alike: https://www.youtube.com/watch?v=xAoljeRJ3lU
The Nirenberg and Matthaei experiment was a scientific experiment performed on May 15, 1961, by Marshall W. Nirenberg and his post doctoral fellow, Heinrich J. Matthaei. The experiment cracked the genetic code by using nucleic acid homopolymers to translate specific amino acids.
The Nirenberg and Leder experiment was a scientific experiment performed in 1964 by Marshall W. Nirenberg and Philip Leder. The experiment elucidated the triplet nature of the genetic code and allowed the remaining ambiguous codons in the genetic code to be deciphered.
The Marshall W. Nirenberg Papers Public Reactions to the Genetic Code, 1961-1968
Since the publication of The Embodied Mind (1991), the cognitive sciences have been turning away from the mind-as-program analogy that dominated early cognitivism towards a conception of cognitive functioning as embodied in a living organism and embedded in an environment. In the past few years, important contributions to embodied-embedded cognitive science can be found in Noe (Action in Perception), Chemero (Radical Embodied Cognitive Scie Rnce), Thompson (Mind in Life), Clark (Being There and Surfing Uncertainty), and Wheeler (Reconstructing the Cognitive World).
Why not?
It’s cruel to be kind, don’t you know?
I read an article on Salon, about a woman who gave birth to a premature baby that didn’t survive. The point of her article was tell everyone how much she hates when people tell her her baby is in Heaven.
But actually her point is more than that. Her point really is to make sure you know that she is atheist. And to tell you, that you are dumb for not being one. Because this is what good atheists do. They talk about how the “great thinkers” like DeGrasse Tyson and Sagan give her comfort, when they reassure her that you are just a tiny speck in a much bigger universe (that has no purpose). Continue reading
This is my suggestion. Lizzie is happy for any participant to author a thread here. Most regulars already have author status which allows them to publish OPs. Other members have contributor status which allows them to compose posts that will be published on request, although author status is available on request to anyone who’d like to have unrestricted (within the rules) ability to publish OPs.
Whilst I think it is great that we have such wide-ranging (and on the whole rancour-free) discussions, the topics do get mixed and hard-to-follow, especially with the annoying page bug.
I invite anyone to start a new thread on a topic that is getting lost in the cross-talk.
I also invite suggestions from our esteemed clientele. Especially welcome would be a suggestion how to fix the page bug.
There are a lot of great resources available on the internet for countering Code Denialism. I’ve gathered a few of them for your convenience. I envision a multi-part series on this topic because the evidence against Code Denialism is so extensive and Code Denialism seems to be surging in popularity here at TSZ.
The 1961 paper by Crick et al. is an outstanding example of the use of thought and logic to solve basic biological problems. In my opinion, it is a superb paper to assign to students in courses because it illustrates how combining knowledge and wisdom can provide answers to important scientific questions.
They demonstrated that three bases of DNA code for one amino acid in the genetic code. The experiment elucidated the nature of gene expression and frame-shift mutations.
…the mutant strains could be made functional again by using proflavin to insert or delete a total of three nucleotides. This proved that the genetic code uses a codon of three DNA bases that corresponds to an amino acid.
“This concept of a phase shift, or a ‘frameshift’ [in the genetic code of an rII gene] as we later called it, was so foreign to people in genetics that we had endless problems trying to explain this work.”
Seems like they still have work to do.
Lots of heat surrounding this question.
My take is that a code must be a system for conveying meaning.
In my view, an essential feature of a code is that it must be abstract and and able to convey novel messages.
DNA fails at he level of abstraction. Whatever “meaning” it conveys cannot be translated into any medium other than chemistry. And not just any abstract chemistry, but the chemistry of this universe.
Without implementing in chemistry, it is impossible to read a DNA message. One cannot predict what a novel DNA string will do.
DNA is a template, not a code.
Go to it.