Sal Cordova's Path to Young Earth Creationism

Introduction

(S. Joshua Swamidass) #1

@stcordova, are you a young earth creationist like Sanford?


John Sanford at the NIH
(John Harshman) #2

You don’t know Sal? The answer to your question is “yes”, though sometimes he goes with “old earth, young life”, which requires him to claim that fossils are much younger than the rocks they’re embeded in and under.


(Salvador Cordova) #3

Dr. Swamidass,

I am a YLC (young life creationist)/YEC like Dr. Sanford.

I was a former evolutionist raised in a Roman Catholic home, and accepted evolution because I saw it in an encylopedia as a child and then studied biology in 9th grade where I came to believe it briefly. I actually thougth the theory was rather beautiful in as much as life would have limitless improvement for eternity…2001 a Space Odyssey was the way I viewed God-guided evolution.

I began to have doubts about evolution because of the problem of consciousness, and then it seemed to me the origin of life was a miracle, hence if I could accept one miracle I could accept others, so for a long part of my life, especially studying physics and engineering I was an OEC, then became an OEC/ID proponent. Somewhere I became an OE/YLC/ID proponent after nearly leaving the Christian faith because of its supposed lack of evidence.

One of the commenters mentioned indirectly (Gerry Jellison) the guy on amazon who supposedly refuted Sanford. Jellison, an evolutionist, ironically inspired me to study physics in grad school where I studied at the MS level Quantum Mechanics, General Relativity, Cosmology, Astrophysics. Jellison and I have been on good terms and know each other personally despite Jellison’s not-so-good relationship with John Sanford.

I actually got invited by YEC physicist John Hartnett to be his PhD student in Australia, but I couldn’t, since at the time my day job was being a senior engineer at MITRE.

Dembski and Marks tried to get me to be the first student working at the Evolutionary Informatics Lab in 2007, but then Baylor shut the lab down, and I went to Johns Hopkins instead in the evening while working at MITRE during the day. The Evolution Informatics Lab re-opened and Winston Ewert succeeded in the slot that had been originally opened for me…

Somewhere in grad school, after much thought, I became a YLC/YEC/ID proponent

I have been mildly critical of Dembski’s CSI, but supportive of Dembski’s views of Steganography. I’ve been mildly critical of one of Kirk Durston’s papers (the same one you’re criticizing), but supportive of another (his PhD dissertation). I’ve been critical of Granville Sewell’s views of Thermodynamics. I’ve been critical of YEC distant starlight solutions, but for secular reasons there are serious astrophysical anomalies.

Both Kirk and I believe the patterns of diversity and similarity in DNA/Proteins are optimized for scientific discovery, essentially Dembski’s steganography. I hope to work with Kirk to further the findings that were warmly received by his PhD committee.

I provided reports to Dr. Sanford of developments at the NIH and then contributed research to his book contested bones regarding Alu elements and LINE-1s. I gave him data on the ENCODE, RoadMap, 4D nucleome, E4 Epistranscriptome etc. projects at the NIH. We collaborated on research into nylonases, which was just meant to be a 2-day project to make an internet essay, but then it evolved into a pre-print “unpublished” paper, but we have explored getting our results published somewhere. Dr. Sanford referenced the pre-print in the NIH abstract of his talk, but then, for lack of time didn’t mention our nylonase work in his talk (not that I thought nylonases were relevant to his point anyway!)

I learned a little about bioinformatic methods and phylogenetic methods at the FAES NIH grad school, and John Harshman has been my informal critic and tutor at TheSkepticalZone. I learned a few things from Dr. Harshman.

I felt reframing the phylogenetic methods would be a way to realize Dembski’s dream of Steganography. Kirk Durston independently arrived at the same views that I had about steganography (though Kirk doesn’t use that term, and maybe the ID community should come up with a new label.)

I’m presently collaborating with others on methods of visualizing Post Translation Modifications in 3D, and hopefully our work will be presented in part at a Biological conference in April of 2019. I’ve been tentatively listed as a co-author.

So, that’s a little bit of my involvement in all this.


(S. Joshua Swamidass) #4

@kirk, do you agree with this characterization of your views?

For reference steganography by Dembski:

10. Steganography
Finally, we come to the research theme that I find most intriguing. Steganography, if you look in the dictionary, is an archaism that was subsequently replaced by the term “cryptography.” Steganography literally means “covered writing.” With the rise of digital computing, however, the term has taken on a new life. Steganography belongs to the field of digital data embedding technologies (DDET), which also include information hiding, steganalysis, watermarking, embedded data extraction, and digital data forensics. Steganography seeks efficient (that is, high data rate) and robust (that is, insensitive to common distortions) algorithms that can embed a high volume of hidden message bits within a cover message (typically imagery, video, or audio) without their presence being detected. Conversely, steganalysis seeks statistical tests that will detect the presence of steganography in a cover message.

Consider now the following possibility: What if organisms instantiate designs that have no functional significance but that nonetheless give biological investigators insight into functional aspects of organisms. Such second-order designs would serve essentially as an “operating manual,” of no use to the organism as such but of use to scientists investigating the organism. Granted, this is a speculative possibility, but there are some preliminary results from the bioinformatics literature that bear it out in relation to the protein-folding problem (such second-order designs appear to be embedded not in a single genome but in a database of homologous genomes from related organisms).

While it makes perfect sense for a designer to throw in an “operating manual” (much as automobile manufacturers include operating manuals with the cars they make), this possibility makes no sense for blind material mechanisms, which cannot anticipate scientific investigators. Research in this area would consist in constructing statistical tests to detect such second-order designs (in other words, steganalysis). Should such second order designs be discovered, the next step would be to seek algorithms for embedding these second-order designs in the organisms. My suspicion is that biological systems do steganography much better than we, and that steganographers will learn a thing or two from biology – though not because natural selection is so clever, but because the designer of these systems is so adept at steganography.

Such second-order steganography would, in my view, provide decisive confirmation for ID. Yet even if it doesn’t pan out, first-order steganography (i.e., the embedding of functional information useful to the organism rather than to a scientific investigator) could also provide strong evidence for ID. For years now evolutionary biologists have told us that the bulk of genomes is junk and that this is due to the sloppiness of the evolutionary process. That is now changing. For instance, Amy Pasquenelli at UCSD, in commenting on long stretches of seemingly barren DNA sequences, asks us to “reconsider the contents of such junk DNA sequences in the light of recent reports that a new class of non-coding RNA genes are scattered, perhaps densely, throughout these animal genomes.” (“MicroRNAs: Deviants no Longer.” Trends in Genetics 18(4) (4 April 2002): 171-3.) ID theorists should be at the forefront in unpacking the information contained within biological systems. If these systems are designed, we can expect the information to be densely packed and multi-layered (save where natural forces have attenuated the information). Dense, multi-layered embedding of information is a prediction of ID.
> http://www.arn.org/docs/dembski/wd_disciplinedscience.htm


(Timothy Horton) #5

Sal, why is dense, multi-layered embedding of information a prediction of ID? Just because an omnipotent Designer could do it that way what about the method forces the Designer to do it that way?


(James McKay) #6

Hi @stcordova,

I think I can understand what your thinking as far as evolution is concerned, but why a young earth? Personally I went through a brief YEC phase in my mid teens, but I abandoned it in favour of OEC partly on the basis of 2 Peter 3:8 and Psalm 90:4, but also because what I saw in young-earth arguments simply didn’t tally with what I was learning about the basic rules and principles of how measurement works. (My A level physics teacher, a curmudgeonly old-school type called Mr “Percy” Pointer, told us right at the start of our very first lesson that physics is “the art of measurement.” It’s not an entirely accurate definition, but it did drum into us that measurement is absolutely foundational to science in general, and physics in particular.)


(Salvador Cordova) #7

Dr. Swamidass,

SPECIFICALLY to your question, neither I nor Michael Behe believe functionality of junkDNA is a prediction of ID, nor do I believe dense information is a prediction of ID. Dembski has said, this so has the Discovery Institute and my friend Casey Luskin. I couldn’t disagree more. ID doesn’t make predictions (contrary to the usual claim) and I don’t think ID is science.

I suspect Dembski is correct that there are secondary patterns optimized as a user manual for humans. I’m undecided and I want to explore the question with Kirk. Kirk studied the question with only 1 protein: Ubiquitin.

I threw on the table Histone 3, which is 99% conserved in multicellular Eukaryotes! What does that mean?

Kirk will be out of pocket for a while to collaborate with me, same with me so maybe we’ll revisit the issue some day. So the question of Histone 3 is still outstanding.

In the meantime, I suspect a tool could be constructed to estimate the location of post-translational modifications. So far the search for this pattern has been inconclusive. I hope to build a collaboration with Cell Signalling Technology, inc. They seem like a cool outfit…

We want such projects to be open source software so Structural Biologists could use it.

So, Kirk and I will hopefully discuss the meaning of his work in relation to Histone 3 and other proteins. We just can’t do it anytime soon.


#8

I suspect there can be a fine line between seeking some steganographic message versus descending into numerology.


(Kirk Durston) #9

@Joshua, at present, I am a little sceptical of the theory that biological organisms contain “second order” information “of no use to the organism … but of use to scientists investigating the organism.” I just haven’t seen anything convincing yet, but am open to it, pending some good evidence.

I do agree with the description of first-order steganography as defined in the article (“the embedding of functional information useful to the organism rather than to a scientific investigator”). For example, as a result of my more recent paper, the information in large protein family MSA’s can be used to gain insight into the sub-domain structure and folding of proteins, but “gaining insight” is not it’s purpose. The purpose of encoding digital information in protein-coding DNA is to build stable, functional protein structures and complexes useful to the cell. What we might learn from it is incidental.

Note: I’m leaving the office in a minute or so and will be gone into the northern wilderness for the next week, so I will be unable to respond to any further comments in a timely way.


(Timothy Horton) #10

Then why in the world do you keep advocating for it??


#11

Is it written in Hebrew?


(Salvador Cordova) #12

James,

I began to suspect YLC (young life, old earth) was true when I began to ask the simple question, “when and how did these creatures fossilize” and what about radiometric and chemical dating?

I’m no longer Catholic but now Reformed Evangelical, but I put higher priority on brute facts than theological ideas, and I don’t get along well with theologians and philosophers and preachers. I attend church, but well, sometimes my relationships are strained because of my dislike of people theologizing stuff…I like archaeologists and scientists better…

The video that concisely echos my doubt of the age of the fossil record is Drama in the Rocks. You can google it and watch it. It is 35 minutes or so long. It leverages a lot of basic physics and mechanics.

Also, some of my phylogenetic research suggests the MRCAs of all creatures is recent and can’t be solved by coalescence models. In Sanford’s NIH talk, he mentioned all RNA viruses being 50,000 years old. Well, I was the one who gave him that data point!!! It was a peer-reviewed paper that came to that conclusion. I’ve suggested someone in the YEC community pounce on this issue hard, because what that paper found is the same anomaly I’m seeing everywhere, but perhaps not so obviously…

What about radiometric dating? It is subtle because some radio metric dates are young, some old, and why are there missing intermediate isotopes?

During my time at Johns Hopkins, I wrote a term paper on the issue of nuclear transmutation (which is related to radiometric dating) and I thought my professor would take my head off for being so heretical. He loved it! Bryan Nickel’s video of Walter Brown’s hydroplate theory and the origin of radiation echo my suspicions well. Walter Brown references the work of the Proton-21 laboratory which showed electrical nuclear transmutation. Because University of Illinois Urbana Champaigne was favorable to Proton-21’s work, I entertained getting a PhD there. The Proton-21 lab unwittingly provided a possible solution to some of the radiometric dating problems and problems of nucleosynthesis.

Ironically, in 2004-2005, after reading Solar System Evolution, by Stuart Ross Taylor, I was no longer convinced the Solar System Evolved. The book was intended to be an anti-YEC treatise, but then every chapter kept saying that the evolution of this or that planet doesn’t square with physics. If Jesus created matter in feeding the 5,000 or made water into wine, I think that’s how the Solar System came to be. I believe that more after reading what was supposed to be a convincing case for Solar System evolution.

My undergrad professor in Quatum Mechanics at GMU in 2004, James Trefil, wrote the chapter in his book on Dark Matter where he outlined “The Five Reasons Galaxies Can’t Exist.” It was part of my journey in rejecting the Big Bang, not to mention another professor at GMU, Menas Kafatos at the Earth and Space Observatory at GMU, disbelieves the Big Bang along with a couple other professors there like Sisur Roy.

So what about Einstein’s relativity and the distant starlight problem? Well, there are reasons independent of YEC to think there are problems with the constancy of light. When I studied the Friedman-Roberston-Walker-Lemaitre solutions to Einstein’s Field Equations, it struck me like total absurdity – like putting negative mass in Newtons 2nd Law and concocting all sorts of nonsense results. What really sealed the deal was when I was studying Guth’s model of inflation where the universe expands at 1000 times the speed of light, I thought to myself, “and I thought YEC had outlandish untestable theories.”

I’ve been lately favorable to Reginald Cahill’s views on relativity. I actually tried to reconstruct a laser interfeormeter to repeat an experiment he did that demonstrated the Aether and Lorenzian relativity. The results were inconclusive. But Cahill’s re-analysis of Michaelson Morely, Dayton Miller’s Experiment, and Roland DeWitte’s Belgacon experiments were very compelling, nevertheless.


(Salvador Cordova) #13

Just because it isn’t science doesn’t mean it isn’t true. I don’t view historical events as science, but I believe certain events to be true.


(S. Joshua Swamidass) #14

2 posts were split to a new topic: The Speed of Light


#16

When it comes to statements about events where science claims to constrain predictions or retrodictions, how does one determine truth? If your approach assigns truth to a statement which contradicts science, why should that approach prevail over science?


(James McKay) #17

Thanks Sal. I had a look at the video last night – seems like some fairly standard YEC arguments. I found it a bit confusing though – at one point it was claiming that smaller sediment particles are found deposited above larger ones, but the next minute it was claiming that it’s the other way around. At any rate, it didn’t cite any references or sources to look up for more information. I’m also not sure how accurate its claims are about the raw evidence itself. Certainly I’ve seen other YEC claims that misrepresent rock formations in the Grand Canyon – Answers in Genesis’s claim about bent rock layers not being fractured is just one example.

My big problem with young-earth claims is, as I said, the way they handle measurements. I first got into YEC round about the time that Barry Setterfield came up with his idea that the speed of light had been decaying. Some of my friends at church were getting all excited about the idea, but I was asking the question, wait a minute, what about the error bars? The historical measurements of the speed of light simply weren’t accurate enough to support the conclusions that he was claiming, and his idea of a cut-off date beyond which the speed of light stopped changing coincided too conveniently with the invention of tools such as the laser and the interferometer, which allowed scientists to measure the speed of light with a high enough precision to blow the gaff on his ideas.

At first I thought that Setterfield’s ideas were maybe a one-off, but unfortunately since then, I’ve found that arguments like that are the rule, not the exception, in young-earth claims. The amounts of salt and sediment in the oceans are two more examples: poorly known quantities with error bars that are simply too large to support the conclusions that they are claiming. There’s also a tendency to exaggerate the extent and significance of errors in conventional dating methods out of all proportion. Take this video here for an example: it suggests that errors of just ±1% in the age of the earth are a valid reason to believe that it could be out by a factor of a million. For comparison, a car’s speedometer has an error of typically ±2.5%. Nobody in their right mind would consider that a valid reason to believe that you could be travelling up the motorway at a quarter of the speed of light when your speedometer was saying you were doing 70 miles an hour.

Then there was the RATE project, which tried to argue that nuclear decay rates could have been different in the recent past. Unfortunately they’re talking about rates having been accelerated by a factor of a billion or so, and they themselves admitted that this would have released enough heat to raise the temperature of the earth’s surface to 22,000°C. At this point I could only throw my hands up in the air and ask myself whether I was actually dealing with real creationists or whether someone had hacked their websites in an attempt to discredit them. It’s complete science fiction.

I must admit I find the whole idea of inflation a bit of a mind-bender myself, and I understand that a minority of cosmologists are a bit sceptical of it. But even if inflation is wrong, it’s still a massive stretch to go from there to squeezing light from the entire visible universe into just six thousand years. Inflation is right at the very limit of what we can measure and reason about, and concerns the scale of the entire universe. Six thousand light years, on the other hand, represents a far, far smaller scale, far, far closer to home, with far, far simpler measurements and equations. To illustrate, here’s a representation of the distant starlight problem in terms of the size of the Milky Way. The red circle illustrates a distance of six thousand light years from the sun:

Now consider: on that scale, with that picture appearing as it does on my laptop screen, the visible universe would be about sixty miles in diameter. Or if you shrunk that picture down to a single pixel, the visible universe would be about twice the diameter of the London Eye.

YECs argue that the distant starlight problem is the same as the horizon problem. But when you consider the differences in scale that we’re talking about, the two don’t even come anywhere close. Again, the same problem: it’s completely detached from the realities of how measurement actually works.


(Blogging Graduate Student) #18

This is the paper, right?

It was published in 2003, and while the paper mentions some of the pitfalls of estimating this age, much research has been done since that clearly show that factors like saturation and selection over long timescales mean that these low estimates of RNA virus origins (from tens of years to thousands of years) are significant underestimates. E.g:

http://rspb.royalsocietypublishing.org/content/281/1786/20140732.short

I was very surprised to hear Sanford mention it in his talk as though 50,000 years was an accurate estimate.


(Salvador Cordova) #19

Thank you for referencing the article, excellent article.

However the corrections mentioned were on the order of millions of years, centuries and millennia, not hundreds of millions of years.

As and aside, I also don’t think ERVs are evolved because of their role in regulation that would require co-evolution with chromatin modifying proteins like KRAB-Zinc Fingers and the chromatin modifying regulatory complexes built around them that target the ERVs for co-regulation of gene sets. Articles about this have come out only in the last year.

On a related note, we thought we knew for example about Alu’s and LINEs, that has changed only in the last few years. Same with Lnc/Linc RNAs like FIRRE.

I think there’s a lot about biology we thought we knew, but don’t.

But to the issue raised about RNA viruses, it points to a larger issue of gene MRCAs for individual species. My cursory reconstruction of some MRCAs based on intra species comparisons of genes point to recent ancestry within each species.

One example was the aaRS genes within each species. The pattern looks plain as day. One might argue the aaRS genes across organisms themselves are ancient, Ok, but why all the individual MRCAs of the aaRS genes within species recent, very recent. Coalescence doesn’t seem like a good explanation because of geographical isolation. I simply haven’t had time to make the case as I’m working on other things.

Also problematic for Universal Common Descent is that all the pFAM or major protein families don’t have universal common ancestor, and neither does anyone else believe all proteins descended from a Universal Common Ancestral protein. So though we may invoke some Universal Common Ancestral Organism, it seems all the major protein families don’t have a traceable common ancestor. I realized this when looking at the NIH CDART databases.

I’ve been recently scanning the NIH CDART conserved domains after I found a paper about “promiscuous domains.” A lot of the Taxonomically Restricted genes would have to have either convergence, gene fusions, or some very well targeted duplication of gene fragments, and then careful reassembly of the gene fragments to stitch together new proteins and protein families. The KRAB-Zinc Fingers are an example many of which apparently co-evolved with ERVs, and the complexes themselves are Taxonomically Restricted.

When I looked at CDART and the families of proteins, it was plain as day proteins couldn’t ALL have a universal common ancestor. My understanding is that even the evolutionary belief is that the major protein families independently evolved, huge numbers of Taxonomically Restricted Proteins. But if that is the case, that doesn’t look much like universal common ancestry, it looks more like special creation to me. The Nested Hiearchies of life could just as well be defined by isolated Taxnomically Restriced Proteins/Genes as it could be defined by individual protein phylogenies. The problem with many protein phylogenies is invocation of Rooting of Trees rather leaving them unrooted, but that is another discussion…

Even if I were not a YEC, I think it is really pre-mature to be making statements as confirmed fact. I believe in YEC at a personal level, but in terms of the data, I think it would be helpful to just wait and see what we find.

I try not to say, “this or that proves YEC” but I will say, “This or that makes YEC more believable to me.” That is my journey from an evolutionist to YLC/YEC. Some ideas were simply more believable than others.

From a science standpoint, to the extent we can make testable prediction, that will make one model more favorable than another. If the human race is decaying, as Dr. Sanford supposes, it would raise doubts in my mind how something as delicate and amazing as the human brain could have evolved in the first place.


(Daniel Ang) #20

@PdotdQ is this true, particularly regarding FLRW? I think it is wrong to say that inflation is “untestable”, as several findings have been put forth supporting or verifying it. (Such as the BICEP2 finding regarding the polarization of the CMB, which turned out to be wrong, but shows that inflation is testable, even if its status is not as rock solid as the Big Bang, for example.)


(Timothy Horton) #21

Do you think historical events can’t be scientifically investigated? How do you think we came by our knowledge of the Chicxulub impactor or our knowledge of Devonian tetrapods?