One of the most brilliant evolutionary biologists of the present day, Richard Sternberg, PhD PhD was ousted and permanently blacklisted by the National Institutes of Health and the Smithsonian Museum for his ID sympathies.
Sternberg is neither a Creationist nor Darwinist but classifies himself as a Process Structuralist which means he is not much involved in the ultimate questions of how things came to be, he just appreciates the amazing patterns of similarity and diversity in biology.
He was labelled by some of his former supporters as an intellectual terrorist after he used his position as editor of a journal to publish an ID-friendly article by Stephen Meyer in 2004. He paid dearly for that decision, and his subsequent dismissal from the NIH and Smithsonian precipitated special investigations by members of Congress and the White House a decade ago. Unfortunately, nothing of consequence was done for Sternberg and he was destroyed professionally and personally.
Despite his circumstances, he continued to publish excellent essays such as the one that highlights the non-random patterns of SINES (presumed by some to be junkDNA) which are present in mice and rats (link below).
To understand his essay, I will describe the essentials of his essay with a parable. Suppose we had two mostly identical stories published. The stories are identical except for the fact that in one version of the story the name of the main character is “Mary” and in the other version, the name of the main character is “Caroline”. Even if the two versions of the stories were generated from the same template, the changes in the two descendant copies could not have been random.
So even if we assume some sort of common descent of the two versions of the story from some ancestral copy, the differences in the versions could not be the result of random copying errors, but very deliberate and methodical changes in the duplication process that created the two versions. This peculiar phenomenon plays out approximately in the genomes of mice and rats, and I call it the Sternberg-Collins paradox in honor of Sternberg who brought the paradox into prominence and Francis Collins who was among the first to comment on the anomaly.
Assume for the sake of argument rats and mice came from a common ancestor. Are there differences which are non-random and thus evidence for non-random mutation? Sternberg effectively answers, “yes”.
The mouse and rat genomes look very similar, but there are sequences that repeat over and over again in each of their respective genomes and mostly in the same corresponding locations. If these sequences were identical in both lineages, there would not be much of an issue, but they are different even though they are in the same general corresponding locations.
Let me call one set of these repeating sequences in the mouse genome “Mary” and the corresponding sequence in the rat genome “Caroline”. The name “Mary” appears in numerous places in the mouse genome, and in the corresponding places where “Mary” appears in the mouse genome, “Caroline” appears in the rat genome.
Of course this was a figurative way of describing what is going on. “Mary” is in reality the B1/B2/B4 set of SINE retro elements in mice, and “Caroline” is in reality the ID SINE retro elements in the mouse. But don’t get hung up on the fancy language, the basic problem of non-random changes from a supposed common ancestor is brutally evident. A graph that shows the non-random changes is here and explained in Sternberg’s essay:
Sternberg’s point is that if mutational events happened, it was non-random, since to suppose it was random is an absurdity in the extreme. It cannot be the result of random DNA copying errors, but some non-random copying mechanism if common descent were true.
Is the non-random pattern the result of natural selection? Sternberg doesn’t address that question. But if the non-random SINE pattern is the result of selection, then this would mean the SINES aren’t junkDNA.
But if natural selection is assumed as the mechanism, there would be issues of the evolvabilty of so many nucleotides simultaneously. We’re talking maybe 300,000 SINE insertions in each lineage! For mice, the B1 sine is about 150bp and homologous to the 300bp primate Alu. The B2 SINE is 190bp. I could not find the size of the rat ID SINE nor the mouse B4 SINE, but I presume they are within the range of most other SINES (75-400 bp).
The source article in Nature which Sternberg referenced and had a buzzillion co-authors can be found here:
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
That article points out:
Despite the different fates of SINE families, the number of SINEs inserted after speciation in each lineage is remarkably similar: approx300,000 copies.
Sternberg highlights the issue of having 300,000 non-random insertions happening in parallel in the two lineages after they split. He lays out the paradox which is the focus of this OP here:
Beginning to Decipher the SINE Signal
FWIW, I suspect there are probably similar issues with the Alu elements that appear in primates. Certainly this would be an issue if the mouse B1 (homologous to primate Alu) is in homologous locations in the primate genome. If that is the case, the Sternberg-Collins paradox is in play as well for primates. Perhaps one day we’ll know for sure if this is the case.
Welcome to TSZ, Dr Swamidass. I’m (pleasantly!) surprised you can find the time.
He’s brilliant because he says things Sal wants to hear.
stcordova,
Ha! That’s exactly what my wife says! Busting his pan trying to get Microfocus COBOL to connect with a MySQL database for a contract I’ve taken on, simultaneously trying to learn songs for a wedding, and write a thesis … time is short at the mo I’m afraid!
That would be human nature, I guess.
I did notice this statement on Sternberg’s website:
…one cannot speak with precision of a gene → homology relation, in the sense of “master genes” or “DNA blueprints” or “genetic programs” that determine cell differentiation, without first clarifying what the “gene side” of that relation stands for.
I guess he means by this that we can’t (yet) predict how an organism might develop, grow and function merely from having knowledge of the full sequence of its genome, or how changes in the genome sequence will cash out in terms of the phenotype.
Whilst I think this is a hugely complex and intriguing problem (for instance, having passed through the bottleneck of a zygote, how does a spider have the innate ability to build webs), it doesn’t mean there isn’t a (physical) solution.
The description of Sternberg is clearly reputation inflation, one of the creationists’ favorite tactics. Do a google scholar search or Web of Science search and you can see that Sternberg’s research is fairly described as “mediocre” in terms of impact.
The description of what happened to Sternberg is clearly misleading, as can be verified by reading Brayton’s article at http://www.skeptic.com/eskeptic/08-04-17/ .
Both par for the course for Cordova.
shallit,
People are supposed to trust a skeptic site to give the unbiased truth about the treatment of someone who doesn’t support their worldview?
Is this some kind of joke, or you just think people are stupid?
As I understand the “theistic evolutionist” position, the GAP within which one may place a deity based on ignorance is narrower. They may have trouble on cosmology sites, but they should incur no wrath here. Their discussions of evolution should be expected to be identical (in relevant respects) to those of non-theistic evolutionists. Appeals to ignorance and zipping on to deities will be equally frowned on, so there shouldn’t be divisable “camps”–except to the extent that one may close a comment with “God bless you”–as though someone has just sneezed.
walto,
Theistic evolution makes absolutely no sense that I can think of. How can a person believe that a completely random, unguided process, that could end up creating any kinds of creatures, or even none at all, would happen to also end up making creatures that have a divine special relationship to a God? If the process ended up simply creating a grey slime, would that grey slime have a special relation to God?
Plus this accidental evolution also created the relatives of Jesus? That sounds like full on nuttery to me. But I am open to hear someone explain their rationale.
phoodoo,
Of course, you got the real unbiased truth from other sources – AiG, ENV, UD or some such. Chortle!
Allan Miller,
So you at least concede my point that a skeptic site won’t give true, unbiased information, right?
Except, of course, the truth about how decisions are made in phoodoo world. That, apparently, is secret.
Are you claiming Ed Brayton got his basic facts wrong? Which facts do you question in Brayton’s report?
Alan Fox,
First things first Allan, are you claiming you can get true, unbiased information from an advertised skeptic site?
It seems Wikipedia is not giving true unbiased information either. So why don’t you pop along and edit that page I linked to? If you can support your edits with facts there won’t be any problems at all keeping those changes around for all time.
I’m interested in this also. Phoodoo, what is the first error on that page?
I don’t think any site that wishes to be taken seriously can get away with regularly reporting falsehoods. I also distinguish between facts that can be verified and opinion based on facts.
TL,DR; Yes!
So does Ed Brayton get any specific facts wrong?
Alan Fox,
Well, see this is exactly the kind of dishonest bullshit I would expect from you. You imply that these other sites you mentioned, are not trustworthy because they have an opinion about evolution that is not the same as yours. And you use this as a counter to the fact that a skeptic site can’t be trusted to tell the truth about what happened to Sternberg.
So in your parceled worldview, you have no problem suggested that a bias makes a site unreliable, BUT ONLY when that bias is one you don’t agree with. When the bias is one you do agree with, OF COURSE they are telling an accurate story.
So why in the world would I go through a long criticism of a ten thousand word hit piece on Meyer and Sternberg, when you have already shown that you deal in ridiculous double standards.
You don’t value academic truth Allan, you are a mouthpiece for your skeptic sides propaganda. You are essentially admitting that here.
Just so. Mung is familiar with the distinction. It appears that his claims need to be carefully scrutinized in the future given his dissembling here.
By the way, welcome to TSZ!
Exactly so. That’s why it is foolish to trust creationists, as opposed to theistic evolutionists, on matters of science.
Dude, I feel your pain.
OMagain,
Wikipedia O’Magain? Jimmy Wales Wikipedia? The atheist preacher Jimmy Wale’s website Wikipedia O’Magain? That Wikipedia??
Gee wiz, You don’t ever feel dirty playing such a whore O’Magain?
?
I merely said facts are open to interpretation. That’s the fun of politics.
I thought you were referring to Ed Brayton. Most, if not all, of his facts can be checked.
Wherever a story sounds, well, unusual as well as interesting, I try and follow back to the original sources. It often becomes less unusual as one gets closer to the original facts.
Entirely up to you. I suggest the facts Brayton highlights are verifiable. Brayton gives his sources.
I value analysis based on correct facts. What is the point of building an argument on falsehood? BTW it’s Alan
Well, my impression is that you asserted that Ed Brayton’s report was biased or incorrect. You seem not to want to support that claim and rather rely on slur and innuendo. Do you think that is profitable?
Then what did this mean Allan?
Alan Fox,
What do you think about this Allan? These are the emails uncovered when investigating his case. Is this inaccurate?
That was from Allan! 😉
I’ve often picked up on an interesting scientific development via Denyse O’Leary at Uncommon Descent. I wouldn’t ever rely on her interpretation of the facts, however. I’d just follow the link to the source.
Regarding Ed Brayton, which of his reported facts do you think are incorrect?
Alan Fox,
I just posted the truth about what happened at the Smithsonian. The emails make it obvious what was going on.
I’m sure the emails exist. I’m sure the quote from some investigation is correct. I question the correctness of Given the attitudes expressed in these emails, scientists who are known to be skeptical of Darwinian theory, whatever their qualifications or research record, cannot expect to receive equal treatment or consideration by NMNH officials.
I suspect that conclusion is overblown. Especially as Sternberg still works at the Smithsonian.
Mung,
You might find out that what you understood to be the story was not the story at all. But I understand why that might be undesirable for you.
I imagine Sternberg’s colleagues were pretty pissed off at him. Other than that, what sanctions did he incur?
When people behave poorly, I’d expect to find ’emails’ talking about that poor behaviour. Would those emails have existed in the first place if Stenberg had not behaved has he had? No.
Seems people are not allowed to talk about their colleagues in less then glowing terms in phoodoo world on official email accounts. I wonder how he came to that decision!
I leave responses to that attack to theists, but the overall landscape of the argument is this: There are truths about living things that you think theories utilizing only natural selection and random mutation can’t explain. But even if that’s true, nothing about God follows from it. Maybe if you start with the view that there’s a “special relationship” between God and his creatures, you have to have a particular picture of how evolution works, but science doesn’t start with that story.
To ‘a’ god? Don’t be coy. You mean a single, specific god. And who knows, perhaps your god creates many universes and only some of those produce creatures that become aware of their creator.
My god is more powerful then your puny god. My god can create universe after universe and not be bothered about if things appear that worship it or not. It does not need the praise of pink tubes of meat. Your puny god however has to explicitly create things that worship it. Divine masturbation, if you will.
I don’t judge Rick by how his former peers viewed him or how much citations he gets by other evolutionary biologists, but by the quality of his work as testified by his bold prediction that Alu’s elements (which compose 11% of the genome) are functional.
So let’s look at the words of one the world’s leading evolutionary biologists (at least by evolutionary biologist’s ranking):
Ah, but that was mere 6 years ago, in 2010. What do we know in light now of laboratory experiments just a few years later? A back of the envelope calculation demonstrates that the Alu units which Ayala considered degenerate trash are now realized to have the potential to collectively implement 10^16 bytes of information in the brain and nervous system.
Here is the supporting documentation. First the computer RAM analogy to Alus as published in the Proceedings of the National Academy of Sciences:
How enormous? For one cell enormous, for a billion cells enormoser!
If there are approximately 1 billion brain cells, and 100 million bits of information being stored in each cell through the Alu-generated transcripts, using a back-of-the envelope calculation, the combined information storage capacity of the Alu-generated transcripts is on the order of : 10^17 bits which is 1.25 x 10^16 bytes. By way of comparison, a recent estimate of the brains storage capacity based on was suggested at 2.5 x 10^15 bytes. From Scientific American:
http://www.scientificamerican.com/article/what-is-the-memory-capacity/
Another news report in 2010 regarding work at the Stanford Universitiy Medical Center:
To paraphrase a proverb, “the junkDNA stone which Ayala rejected turned out to be the chief cornerstone junkDNA.”
That’s why I judge Rick to be brilliant, he disputed Ayala on the nature of Alus and it looks like Rick is winning this round of the exchange. So what if he’s mostly ignored, Sternberg may be obscure but he is right which is better than being famous like Ayala and dead wrong.
Revisiting the transposases issue….
Rumraket in the “Evolution Visualized” thread gave one of the best comments I’ve seen. He suggested the mysterious SINE pattern that illustrates the Sternberg-Collins paradox could have a chemical basis. That actually echoed my personal suspicions, and hence I felt I wanted to put the issue on the table.
It is well known that proteins which operate on DNA can have binding affinities which would make them more likely to operate on some parts of DNA rather than others. That is why the suggestion that transposases causing preferential insertion sites cannot be ruled out for the magical SINE pattern IF (and a big IF) SINEs were inserted by transposases.
It turns out, that the insertion mechanisms of SINES is not transposases, but rather reverse transcriptases.
So, yes, I could not in good conscience rule out a chemical basis for the SINE pattern if transposases inserted SINES, but then on further investigation, there appears to be an error in supposing transposases operate on SINES in the first place!
This is attested to by the Wiki article on transposable elements and several other biology sources.
The insertion of SINES apparently happens where there are chromatin breaks and a randomly floating reverse transcriptase puts them in there. If the chromatin breaks are random, then the SINE patterns should be random. One could postulate the chromatin breaks are non-random, but the I found a remark in passing that said that any preference of SINE insertions (in the lab, not in phylogenetic speculations) is not well known any way.
SINES are class 1 transposable elements, the class 2 transposable elements (TE) do have some non-random binding preference, and it is class 2 TE’s that are relocated (“jumping”) by transposase.
But since SINES are class 1, not class 2, so transposase can’t be the explanation for the Sternberg-Collins paradox. At best one has to appeal to non-random chromosome breaking patterns, that “just so” happens to also create functional SINES.
I would love to see your math here. 10^16 bytes is 10 billion megabytes (or 10 million gigabytes). This sounds amazing.
What is your theory on how genomes manage to compress this down to about 2 gigabytes of DNA? If you are rigth, DNA has magical compression powers entirely beyond anything we have ever seen. In fact, it falsifies information theory. Does that now end Lennox’s “Semiotic” argument against evolution? And all the other “information theory” arguments against evolution?
Class 1 elements are also enzyme catalyzed and this can (almost certainly does) have a non uniform distribution https://en.wikipedia.org/wiki/Retrotransposon
In fact, it is nearly impossible to construct a biological system with uniform random behavior. This is no exception. One thing that could explain the preference for peri-coding regions is “DNA structure”, a well known modifier of DNA insertions.
I take a pretty standard Christian position here. I believe God makes himself known to the world by raising Jesus from the dead. Encountering Him here, I see no reason for ID arguments for God. I do science to understand His creation, not to prove He did it. Using science to prove God’s existence seems very insecure, and theologically suspect, to me.
A quick note to the non-religious here. If your main exposure to Christian thought is ID proponents and “creationists”, I can see why you might be confused about Christian theology. Quite often (though certainly not always), there explanations of theology are about as clear and accurate as their understanding of science.
In particular, several anti-evolutionists make a great deal of hay about “randomness” in scientific theories being totally incompatible with belief in God. This is entirely absurd, and no serious Christian thinker agrees with that. Frankly, they are not even consistent on this, because I have yet to see anyone complaining about randomness (for example) in embryology as reason to reject science there.
Usually (it seems) what is going on is that they start with opposition to evolution, but then reshape both their science and theology in service of that hunt. So, with some important exceptions, I would doubt the theology they present as much as you might doubt their science. If you want to understand Christianity, talk to a Christian who is more thoughtful, and isn’t on the hunt for the evolution “white whale.”
The Cold Spring Harbor Labs paper says an individual cell’s genome has 100 million A-to-I editable sites. We don’t exactly know how it is used yet, we are learning, but we do know when we knock out the ADAR enzyme that enables A-to-I editing, it causes brain damage (seizures and other things) for one class of ADAR knockouts and is lethal for other classes of ADAR knockouts.
We also know we have 1 billion brain cells with separate genomes and transcriptomes created through LINE1 activity (as shown by the Salk laboratory in Sept 12, 2016 Nature Neuroscience).
With these facts a back-of-the-envelope calculations follows:
100 million bits/cell x 1 billion cells x 1 byte/ 8 bits = 1.25 x 10^16 bytes ~= 10^16 bytes
Also, the Chromatin has nucleosomes that are spaced about 200bp apart (the nucleosome wraps around 147bp DNA, but the spacing is 200 bp apart). There are 42 histone states on all 4 classes of canonical histones (H2, H2A, H3, H4) which is roughly 42 bits (a bit more because of trimethylations, etc.).
3.3 giga base pairs x 1 nucleosome/ 200 base pairs x 42/nucleosome =
693 million bits per cell
1 billion cells x 693 million bits/cell = 6.93 x 10^17 bits ~= 10^17 bytes in the brain
A similar calculation can be derived for the chromatin CpG methylation marks and is a similar order of magnitude.
The Stem Cells Handbook of 2014 calls the chromatin modifications (histone and CpG methylation) “cellular RAM”. There is the emerging science of “epigenetic memory” which relates chromatin modifications to learning and cognition.
Now we see a complex machine composed of LINE1, Alu SINES, chromatin modifications supporting 10^15 bytes of storage in the brain (the Scientific American article estimate. Not included in this is the mysterious role of the glycome which we don’t have good data on because of sequencing difficulties.
3.3 giga base pairs of DNA translates to :
3.3 giga base pairs x 2 bits/ base pair = 6.6 gigabits
6.6 giga bits x 1 byte/8 bits = 820 million bytes of Shannon information
One of the answers is the LINE-1 which causes each neuron to have a different genome and transcriptome. It is what can be described as self-modifying code and lossy decompression.
An MP3 audio file can be lossy decompressed into a large number of valid forms, a self-modifying program can probably decompress to some unimaginable range of possibilities.
The LINE-1’s and Alu SINES in the brain implement apparently both of these concepts. We are “fearfully and wonderfully made”. Imho, we and our genomes aren’t mostly junk (except for the degeneration that happened because of the curse on Adam), we are fearfully and wonderfully made.
I don’t follow Lennox at all! So I can’t say, sorry.
phoodoo,
No. It’s entirely possible that a ‘skeptic site’ would give true unbiased information. It’s also entirely possible that a Creationist one would.
But you lot and your constant whingeing about Sternberg, Shapiro and whatever other maverick you think supports your cause … Jeez. It’s not about frigging prophets.
phoodoo,
I think you might be confusing your Al(l)ans.
stcordova,
So I see your math now. Respectfully, it is wrong. These are not the right formulas. I think you forget that most of the DNA is identical across multiple cells and that most DNA is not variant. At best, you are calculating a grossly inflated upper-bound on information, but forgetting that most of that storage is just lots and lots of copies of the same thing, or modifications based on simple “rules” (e.g. the behavior of ADAR).
It is a good thing you are wrong on your math. If you were right, and could prove it, you would have disproven information theory.
stcordova,
The ‘nonrandom’ distribution is more down to the accessibility of heterochromatin vs euchromatin – a physical rather than ‘chemical’ mechanism, not massively dependent on the particular mode of transfer.
Patrick,
Yeah, when I see a software engineer claiming to have some special insight into ‘design’, I feel the urge to hit something …
Dr. Swamidass,
Also respectfully in reciprocity. The DNA Alu regions I was referring, which generate RNA transcripts, create RNA transcripts that are changeable, not fixed.
That is the significance of A-to-I editing mediated by the ADAR enzyme where the Adenine positions in the Alu DNA correspond to Adenosine positions in the RNA transcript which can be edited to either Adenosine or Inosine.
It is incorrect to assume the final Alu RNA transcripts from Alus are always matching the DNA Alu sections from which they are first generated. They are edited. That was the point of the Cold Spring Harbor deep RNA-seq project that detected the variety of Alu generated RNA transcripts. The Alus may be repetitive in the genome, but they aren’t in the transcriptome. And when this editing capability is knocked out, it causes neural disorders or death.
The figure of Alu-generated RNA positions that are editable is 100 million bases. There are 3.3 gig base pairs of 6.6 million bases of DNA. One paper I referenced specifically said:
My formulas reflect the potential of variability in the Alu generated RNA transcripts, not the DNA Alu sequences. But this still implies the Alu’s aren’t junk, they are pretty important, and that was also the conclusion of the researchers as well.
My numbers are derived from accepted literature and respected laboratories like Cold Spring Harbor.
Also, as pointed out in the Nature September 12, 2016, the genomes of each neuron are not identical because the LINE-1’s in the somatic cells change the genomes in each cell.
The DNA is not invariant in neural cells, that’s why the discovery of the Salk Institute was big news, they confirmed this and also confirmed the role of LINE-1 (previously assumed to be junk also) in the generation of separate genomes in each neural cell.
Here is the report again in Salk Institute:
I can understand why Dr. Ayala thinks Alu are junk because new Alu insertion mutations are bad. This raises the question why existing Alus are so amazingly functional ( if Cold Spring Harbor labs is correct).
What does this sentence mean? I don’t know what you are trying to say a serious Christian doesn’t agree with. I don’t even know what you mean by a serious Christian thinker.
Furthermore, unless you have your own special meaning about what a serious Christian thinker is, I am pretty sure many many people who consider themselves to be serious Christian thinkers believe there is a divine relationship between man and God, which is unique and separate from all other living things.
This of course would logically be completely contradictory with a Darwinian theory of evolution, that has no guidance or plan, and which defintionally can make no clear distinction between man and earlier forms.
OK, I’ll give it a shot.
To me, this answer is about as clear as Swamidass’s answer to Mung about Jesus. Which is to say, not clear at all to me. Perhaps others know what you are saying here?
Some people might also think that creating evolution to make man, would be called tinkering, if creating evolution means it will make a man.
I am starting to understand why evolutionists run away from their random aspect so terrifiedly.
Interesting thoughts.
First, I would say that the Darwinian theory of evolution (defined as positive selection dominated change) was falsified a long time ago, in the late 1960s and 1970s with neutral theory. Neutral drift turns out to be quantitatively more important to explaining most features of genetic evolution. This isn’t to deny the importance of positive selection (it still exists and is important) but it is not the dominant mechanism.
Second, even within in a purely scientific and evolutionary viewpoint, it is possible to recognize the difference between humans and other animals. This isn’t to deny our continuity with the animal kingdom, but also to affirm our discontinuity too. See this video of me with a leading evolutionary biologist discussing exactly this point: http://peacefulscience.org/more-than-apes/.
Third, if we drop “Darwinian” to just refer to the current modern synthesis of evolutionary theory, you are right that the scientific account does not find any evidence of direction or planning. I agree with you here and do not dispute this.
So the question becomes, really, is it possible that God could have created a process (like evolution) with a purposeful intent that science could not detect? I think the answer here is obvious. Of course He could. In fact, I would say, unless He wanted us to discern His purpose, we could not.
In my view, then, evolution has a purpose in creating us. Science itself cannot uncover its purpose. I find that out by other means.
Well thanks for the warm welcome to all. You guys have been (pleasantly!) surprisingly nice. So that makes it worth it. Of course, I gotta lot of work on my plate, so not sure how long I will be around.