Smashwords discounts my e-books in July

Posted on July 7, 2021 by Tom Hopp

Just so’s you’ll know, Smashwords, one of my two book publishers, is having a month-long sale this July—that would be right now! Some titles are free, like my ever-popular novel Rainier Erupts! and my personal favorite short story, “A Dangerous Breed.” Other titles are half-off, so check them out on my Smashwords Author Page.

Even if you routinely use only Kindle, iBooks, or Nook, you can grab versions on Smashwords that are compatible with those devices, so don’t be afraid. Save that fear for gripping action tales like The Great Seattle Earthquake and The Smallpox Incident, which are participating in the festivities at 50% off.

Smashwords is the class act of independent publishing, so if you’ve never stopped by, now might be the time. One word of caution: check that the “filtering” pulldown on the righthand side of the menu bar is set to “exclude erotica” because Smashwords is pretty easy on authors of, shall we say, “naughty” storytelling? But with the filter on (it usually is) you won’t even see them. Ta Dah! You’ll still see bodice-ripping and pect-rippling romance titles, if that’s your thing, but nothing more tawdry than that.But I digress, given none of my books are in either category. On the other hand, if you want red-hot-action-adventures, medical thrillers, or laser-blasting science fiction stories, then you’ll want to take a fresh look at my titles while many are on sale.

And that about covers it. Happy reading!

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Eek! I dreamed up deadly mutant viruses long before COVID-19

Posted on May 8, 2021 by Tom Hopp

Just as you get nice and immunized with COVID-19 vaccine, along comes a new terror—the viral variant! Deadlier strains of COVID are cropping up with alarming frequency. Such mutational shifts allow the new viruses to circumvent the immunity you acquired with your hard-won vaccination. So, are we doomed?

If it’s any consolation, this “variant” phenomenon is nothing new. Virologists have studied it for decades. Variants were first described among the influenza viruses of the great pandemic of 1918, in which they played a role in drawing out the pestilence for several years. And they’ve cropped up in every epidemic since. So even the frightfully named “Eek!” variant of COVID is not an entirely new concept.

But as we watch with dismay, this and other variants are arising around the globe with increasing frequency. So, it’s a cold comfort to know that they’re nothing new under the sun. Somehow, even the knowledge that humanity survived not just each new pandemic, but all the variant strains that piled onto previous plagues, is not entirely satisfying. Not when the virus threatens you and yours on a daily basis. Histories and statistics of mankind’s recovery from previous epidemics can’t help you shake the fear that, well, you might not be counted among the living when all is said and done.

So what’s this got to do with my fiction? Well, quite a bit, really. I anticipated this phenomenon in both of my epidemic novels, The Smallpox Incident and The Neah Virus. In each story, I laid out realistic scenarios based on my career-long studies of viruses and vaccines. My intent both times was to dramatize the social upheavals and desperate responses of medical and government agencies trying to avert catastrophe. Unsurprisingly to me, many events I portrayed have come true in the present emergency.

I also addressed the dire question, “Did this virus arise out of nature, or is it an escaped laboratory monster?” Without giving away too much let me just say, in one book the answer is “yes” and in the other the answer is even more unnerving. But one nice thing about fiction is that such questions can be examined carefully, and then answered clearly. No lingering doubts remain in the last pages of The Smallpox Incident or The Neah Virus. Don’t you wish life could imitate art in present circumstances?

Might I suggest you grab a copy on one or both of these now classic books, so you can read and reflect on the notion that nothing happening today is so terribly unheard of by scientists like me, who study viruses and vaccines? An added bonus is that my stories have relatively happy endings given the dire circumstances—and that’s the sort of outcome we all hope for in these trying times.

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The Great Shakeout–Will Seattle’s Tsunami Chimes Ring?

Posted on October 13, 2020 by Tom Hopp

I’ve a mind to drive downtown on Thursday October 15 at 10:15 AM and roll down my car window. I’d like to hear the sound of the tsunami chimes ringing out. Wouldn’t you?

Seattle, and the whole nation for that matter, is preparing for the “Great Shakeout” earthquake drill scheduled then. I’m registered to participate as an individual who’s ready to get “all shook up,” along with many Seattleites in all walks of life and diverse places of school, work, or what-have-you.

This year, I’ve picked out tsunami preparedness as my special area of concern. This comes in response to things I learned while researching my novel, The Great Seattle Earthquake, published last year. You see, when I looked into the idea of a major quake striking right underfoot on the Seattle Fault, I learned that, in addition to the trauma and loss of life that would come from such a natural disaster, the threat of a devastating tsunami has been pretty well established by recent scientific studies. So, that leaves me wondering, are Seattle’s emergency planners covering this possibility adequately, or at all?

My research left me, well, just a little worried that the answer is “kind of.” As I wrote a year ago, I found the tsunami preparedness plan for our two waterfront stadiums definitely less-than-adequate. Here’s a link to that older article. This year, I’ve been wandering around the internet trying to glean any news about an improved stadium plan, but so far I’ve found nothing at all. That’s a step up, in my opinion, because the old plan told people to calmly exit the stadiums, which might mean tens of thousands of people walking straight into an oncoming tidal wave. So, the good news is, I didn’t find any of that old misinformation in the present plans. I guess maybe my blog did some good, somehow. On the other hand, what I found was–nothing at all.

But I did find an old Seattle Post Intelligencer article from 2005 describing the installation of the waterfront warning system shown above. According to that article, this is what you’ll hear in an emergency:

“The first thing will be a tone that’s an attention getter so people will listen,” Steve Marten, project manager said. “We’ve chosen the Westminster chimes.”

“That will be followed by an actual voice that will give a specific message so that we can direct people to do what they need to do to get out of harm’s way.”

Hopefully, 15 years later, this system is still in operation and ready to deliver the message, “Run like hell for high ground!” But I haven’t found much information about it other than the old article. Let’s hope it’s currently in place and in the hands of people who are ready to deliver the life-saving message.

As I portrayed vividly in my novel, folks in the stadium area will have only a few minutes to make up their minds whether they’ll flee to safety–or die.

So, yeah. I think I’ll drive downtown Thursday morning and find out how well the system is working.

Update October 16, 2020: I did like I said and went down to the waterfront and listened as 10:15 came and went without a sound. I stood there on Ivar’s Pier 54, staring at the Fireboat Leschi, which figures so prominently in The Great Seattle Earthquake, moored next door at Fire Station Number Five. I noticed that the alarm speakers shown above had been removed. But I can’t help but wonder. In the event of a quake on the Seattle Fault, those loudspeakers would be lifesavers. So, where did they go?

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I Dreamed the Bridge Fell Down

Posted on August 15, 2020 by Tom Hopp

This photo of the West Seattle Freeway Bridge shows you two things: 1. It’s a marvel of modern engineering, a huge construct of reenforced concrete that crosses the Duwamish River in a single arching high-rise span. 2. It’s empty of cars, trucks, or even a bicycle.

That’s what happens when such a modern marvel suddenly develops a profusion of cracks at mid-span, threatening to plunge the whole thing into the river along with any vehicles and people unfortunate enough to be crossing at the time.

So it’s closed for repairs, or for demolition, if repairs can’t be made solidly enough to guarantee public safety. This closure has altered the commute from West Seattle to downtown from easy compared to other commutes, to a routine nightmare for those needing to cross the river daily.

So what’s all this got to do with me and my novels, you might ask. The answer is pretty simple: I predicted the demise of the West Seattle Bridge in The Great Seattle Earthquake. I dramatized just what it would be like if you were driving across the bridge when disaster struck. A scary ride, to say the least, with your survival in serious doubt. And all this written several years before anyone noticed that the bridge had begun to develop cracks at midspan–for real.

Now, I don’t claim to be clairvoyant—just a thorough researcher when getting background information for my stories. But this isn’t the first time my fiction has touched upon things that later became fact. This sort of prognostication seems to be a hallmark of my writing these days. My publisher’s website describes me this way: “Thomas P. Hopp routinely imagines the unimaginable.” And that’s definitely true in this case. No one had seriously considered what might happen if the bridge split in the middle and fell—no one except me, it seems.

While researching my stories, I tend to uncover obscure factual details that stimulate me to think through the worst-case scenarios. I portray these in my stories and let the reader follow characters whose lives are shattered or at least radically altered by the new threat. The Great Seattle Earthquake is the latest in a series of disaster novels—natural or otherwise—that I’ve published. Previously, there was Rainier Erupts, in which the characters will either live or die depending on minute-to-minute—or second-to-second—decisions made when our local mega-volcano blows its top. Then there’s my medical thriller, The Neah Virus, in which a brand new virus arises out of nature to spread contagion and death, precipitating a desperate quest for a vaccine. That ought to sound familiar. In The Smallpox Incident, the viral nemesis is a laboratory creation of bioterrorists. Does that sound like fears being voiced about COVID-19? For me, none of these ideas are new. I’ve thought them through and published them years ago.

Click the links if you’d like to learn more about my stories. Given the darkness of our times, you’ll be happy to know I tend to follow survivors, not victims. And I’m an optimist who avoids apocalyptic doom and gloom. I try to offer good, scary stories for these tough times, with positive outcomes and even some happy endings scattered amid the wreckage.

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Eerie parallels: COVID-19 & my medical thriller The Neah Virus

Posted on June 17, 2020 by Tom Hopp

When I released my novel The Neah Virus back in 2013, there was little reason to suspect I was writing about issues we’d all be facing in 2020. But here we are, locked down–some of us–and hearing daily of a deadly nemesis that apparently arose among wild animals and made the leap from them to us. With horrendous consequences. And no end in sight (though as a vaccine researcher, I’m optimistic a cure is around the corner).

In my book, a virus emerges from nature at Neah Bay, a small Native American reservation town at the northwest tip of the Olympic Peninsula here in Washington State. People start dying. Contagion is rampant. The Centers for Disease Control calls for desperate measures, including quarantines that require the National Guard to intervene in the interest of public safety. Does any of this sound familiar?

Want more parallels? The virus in my story is a mutant, an altered form of the already deadly rabies virus, changed into an even more lethal and fast-spreading form. Sound familiar?

This is the sort of thinking that wakes me up at night and gets my fingers flying over the keyboard. Given my history of working on vaccines and immune-system hormones over an entire scientific career, I suppose it’s not too surprising. But with that background, when the imagination gets into overdrive, I come up with some pretty scary stuff. Scary to me, let alone an unsuspecting reader.

Consider this short excerpt:

“Once you’ve read the virus’s code, how many days will it take to make a vaccine?”

“The same rules apply as for other viruses,” McKean said gravely. “It takes months to produce each year’s influenza vaccine, and that’s a virus we have a lot of experience with. Given an unknown virus like this, it might take years to create a new vaccine.”

“Years! Isn’t there a shortcut?”

“We could try producing the virus’s surface protein in a bacterial culture—a subunit vaccine. That might be accomplished in weeks or months.”

“But that might be too late for us, if we’ve been exposed.”

His expression darkened. “Kay Erwin told me this morning the number of people with symptoms like Pete Whitehall’s has grown to eighty. That’s enough to convince me the virus is dangerous, even if the CDC still isn’t sure. How have you been feeling, Fin?”

End quote. Now, that’s what we’ve been hearing about the coronavirus–months to years before we have a vaccine. Yikes.

But here’s a nice thing about fiction: if the writer insists on a happy ending (or at least a non-lethal ending) then that’s what you get.

Here’s a link to more information about The Neah Virus if you’re interested.

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Formulating COVID-19 Synthetic Vaccine Doses

Posted on April 9, 2020 by Tom Hopp

This is my third and final post describing a COVID-19 synthetic vaccine. Future posts will return to the usual fare of books, stories, and anecdotes. But this last serious post wraps up a full disclosure of how to make a COVID-19 vaccine, so here goes.

The thing is, you can’t just make a vaccine. You have to inject it, and it has to immunize. So the last step in this process is called formulation. I’ve formulated injectables for–let’s see–about 47 years now, so I ought to know how. Shown at left is a photo of the most recent vaccine I worked on, an anti-cancer vaccine targeting the hormone hCG (there are links below for more information about it).

But before I get into formulation details, let me show you just how well these vaccines work. The graph at right shows an hCG synthetic-peptide vaccination (black arrow) that raised high levels of anti-cancer antibodies within just three weeks and increased by a thousand-fold a few weeks after that. High antibody levels persisted for six months and probably lasted more than a year, though the experiment was ended before that. The two white insets show ISMS (injection site macro-pathology scores) at or below 1.0, which the FDA defines as very little ouch going on. Wouldn’t you like to be protected for six months to a year from COVID-19 right about now? I know I would. By next year, COVID-19 may have done its damage and disappeared, only to be replaced by some new threat coming along. No worries though, we can always make a whole new synthetic peptide targeting the next microbe in three days.

All vaccines are formulated with some added materials (adjuvants) that aid the immune response by creating a depot of material that stays at the injection site for weeks or months. All the while white blood cells come and go, getting more and more riled up and producing more and more antibodies. There are dozens of formulation components out there, and most immunology labs have some on hand. I’ve used quite a number of them myself. Things like alum, squalene oil, gels, and mineral powders, plus immunostimulants like muramyl dipeptide or cytokines thrown in for good measure. It’s a bit of a grab bag of possibilities, but most immunology labs have these things or can get them. The slowest step is to test them in a quality assurance (QA) program to guarantee their safety–but what I’m talking about here assumes you’ve already got the materials certified clean and ready-to-go.

So let me be specific here, because there are many ways to do things wrong, and only a few ways to get the right blend of immune-enhancing ingredients. Here’s my favorite formula (you can skip this part if you don’t have a PhD in biochemistry):

  1. Solid immunogen
  • Peptide-DT conjugate: 0.5 grams
  • Calcium sulfate hemihydrate: 2.0 grams
  • Dextran sulfate (Na): 0.15 grams
  • Water: 1.5 grams (ccs)

Mix these to a thick suspension, dry to a solid block, grind to a fine white powder, sieve to 45-to-150 micrometer particles.

  1. Water-in-oil emulsion

Suspend the fine powder in saline containing 0.125 mg/mL nor-muramyl dipeptide (an immunostimulant). Combine two parts of this with three parts of emulsion oil (squalene + mannide mono-oleate 4:1) and mix vigorously. Your vaccine emulsion is ready to inject!

That wasn’t so bad now, was it? Many vaccine labs have the chemicals and equipment on hand to do this. The next step is animal testing by immunizing white rabbits or mice. These doses can be prepared quickly as shown below, where an emulsion is being made by pushing back and forth between two syringes until your thumbs ache.

For human dose preparation, industrial emulsion-makers, large-scale sterile facilities, and other quality-control techniques are required. No one wants to give a dose of one microbe while protecting against another.

So there you have it. We’ve made our peptide conjugate, mixed in our favorite adjuvants, and now we’re ready to vaccinate a lot of people. The benchtop recipe above could dose five to ten thousand people, and the process can be scaled up to industrial strength for hundreds of thousands or millions of doses. But in the short term, wouldn’t it be nice to use smaller batches to protect hospital staff from getting or giving the virus, as well as first responders and other at-risk people? With this vaccine, all of that can happen within a timespan of a few weeks to a few months, depending on whether you take a little time off to sleep. Given the viral threat hanging over us, who’s really sleeping all that much these days anyway?

Please don’t let the conversational tone I use here fool you. I’m quite serious about this vaccine. Deadly serious, given COVID-19 is out there killing people and this vaccine could be saving lives right now. It’s just that I’m retired and don’t have a laboratory of my own. It might take me months-to-years just to find a funding source and begin operations. On the other hand, there are many organizations around the world that have the right facilities and personnel to make this happen.

My task is finding them and convincing them to give this method a try. Wish me luck.

Below are links for more detail on this kind of vaccine. If you wade through the data in links 2 and 3, you will see that my colleagues and I have made this type of vaccine work in humans before.

  1. First, a link back to my previous COVID-19 postings on my blog site. You can learn a lot about my scientific background by visiting my home page and wandering its links (contact info too).
  2. An old business plan for CG Therapeutics Inc., with details of our cancer vaccine clinical trials (a large pdf, give it time to download).
  3. An old slideshow on CG Therapeutics’ technology with even more vaccine details (a larger pdf).

I have even more information, including a full IND (Investigational New Drug) application that I helped prepare for the now-defunct CG Therapeutics. It wouldn’t take long to repurpose that 319-page document to present this COVID-19 vaccine to the FDA. Any takers?

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Recipe for making COVID-19 vaccine in three days

Posted on April 6, 2020 by Tom Hopp

In my previous post I gave a general outline as to how to make a COVID-19 vaccine in three days. Today I’d like to lay out the plan in fine detail. Pay attention. Everything you need to synthesize an effective COVID-19 vaccine is right here in this post. Of course, you’ll need a sterile, fully equipped immunochemistry lab with quality-control procedures in place to do it—but there are, after all, several thousand such labs around the world. You know who you are…

Take a moment to glance over the image above. It is the “formula” for my vaccine as they say in science fiction movies. However, this is documented science fact, as I explained in the previous post. The loop of circled amino acids represents a disembodied fragment of the virus’s surface “spike” protein. According to the Hopp and Woods computer method, this is THE most likely place for antibodies to bind the virus and kill it.

In this case, however, the fragment has been tamed and made to serve humanity rather than kill. Working clockwise down from the viral antigen loop at the top, you see a chemical linker, a maleimido-caproyl group that attaches the virus sequence to the other major component of the vaccine, diphtheria toxoid (DT).

Diphtheria toxoid is a component of the childhood vaccine, DPT, which gives long-lived immunity against the Corynebacterium diphtheriae microbe, whooping cough’s Bordetella pertussis bacterium, and lockjaw toxin made by Clostridium tetani. The DT protein component of that vaccine is a potent immunostimulant in its own right, and that’s why it’s been recruited for use with Hopp and Woods vaccines. As proteins go, it has the twin assets of being very foreign to the human body, and very large—by molecular standards. Both these qualities, foreignness and “bigness” result in the body getting a raging inflammatory reaction whenever it encounters DT. So a great way to deliver a Hopp and Woods peptide, which is a relatively small molecule, is to attach it to a big nasty monster molecule like DT. The attachment is made via the maleimido-caproyl link hooking on to one of the many “lysine” side chains of the DT molecule (lysine being the amino acid of food supplement fame, by the way).

So here’s an image of the full embodiment of a Hopp and Woods vaccine, in fact two examples. As you can see, the synthesis procedure hooks multiple copies of the vaccine peptide onto each single copy of the DT molecule. It is this rather dangerous looking thing that your white blood cells react to angrily when they encounter it.

There’s a reason why I’m showing two different DT conjugates here. Imagine that the blue-studded DT has the first peptide I showed above attached to it. There’s no reason a lab couldn’t make another, different piece of the virus and attach it to DT as well, to make a second version of the vaccine. Then, if you inject both simultaneously, you get double the chances of having a strong, protective antibody response.

Here’s a second immunogen I came up with. It was picked out by a souped-up version of my computerized analysis of the virus by what I call my HYDRO4 procedure (too much detail?). Anyway, you can see that the same mechanism of attaching to DT is used, but the peptide sequence is entirely different. It’s also not a loop, but rather a linear snake-like sequence of amino acids. I’ve used many looped and/or linear peptides over a long career of making such things, and I think both have their merits.

So, where do we go from here? I don’t have a peptide synthesizer anymore. If I had one, it would be running right now. Actually, it would have long since finished and we’d probably be dosing patients by now. But I’m retired and Hopp and Woods vaccines have languished through lack of interest by government funding agencies and corporate moguls. So here I sit, typing away. And there’s a certain power in that. I long ago published this whole concept in a work of fiction, my medical thriller novel The Smallpox Incident. In that story a biotech researcher who does have a peptide synthesizer gets infected by genetically altered smallpox virus in the hands of bioterrorists. He has to save himself (and humanity) by doing just what I’ve outlined above. So I foresaw the desperate, need-a-vaccine-yesterday scenario we find ourselves in now.

But truth can be stranger than fiction. With my novel as a guide to how to do it, I have been ready for this day to become a grim reality for nearly twenty years. Does anybody out there want to give this a try? This post gives you every bit of information you need to create a Hopp and Woods vaccine for COVID-19. All you need is a peptide synthesizer and a couple other pieces of scientific equipment in a sterile manufacturing environment. Then a vaccine could be in-hand—or in-arm—within a matter of days. Realistically, it would take a week or two to assure that the vaccine was made properly, and then much longer to get government agencies to approve the product for use in humans. But suppose they were tipped off the day you started the synthesis and they also worked day and night to provide the necessary approvals? It could be done.

Several people have gotten back to me suggesting I get in touch with this billionaire or that senator, or this foundation or that government agency. All I can tell you is I’ve been there done that for several other vaccines, long since. It’s a slow process. But I know that out there somewhere is someone with the lab facilities and the ability to make a batch of this vaccine–say, 20,000 doses, starting tonight.

And, be aware that I’ll have one more post on this subject coming in the next few days. I’ve learned several tricks on how to make very efficacious dose formulations to go into the syringe and I’ll gladly share those. Few people know how to soup up a vaccine like I do.

Truth is, I’m trying to reach past the government officials and gatekeepers to get to the people who can actually do this work. It’s a big world and there are many qualified vaccine production labs. So do us all a favor, folks. Pass this post along. Sooner or later (hopefully sooner) it will land in the right pair of hands.

This is Part Two of a three-part posting about the vaccine. Here are convenient links to:

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My Old Neglected Vaccine Could Nail COVID-19

Posted on April 2, 2020 by Tom Hopp

Humanity versus the coronavirus. Who’s winning? So far, advantage COVID-19. But things could change rapidly for the better if a scientific procedure I published 39 years ago is dusted off and brought to bear on this new nemesis. What we lack right now is a vaccine that can stimulate antibodies in our bloodstreams like the one at left, shown grabbing onto a surface molecule of the SARS virus. Remember that bug? In 2003 Severe Acute Respiratory Syndrome killed quite a few people, though its pandemic was smalltime compared to what we’re facing now. After ten years or so, scientists got a look at this anti-SARS antibody (the white and blue strands) clutching the viral protein (red strands) that gives coronaviruses their spiky appearance. It was a tour-de-force of science to get that image, but of course it came a decade too late to help anyone. So, is there anything we can do to hasten the process this time around?

There is.

Ever heard of the “Hopp and Woods Hydrophilicity Analysis Method?” No. I suppose not, unless you’re a scientist—and then only if you’re a vaccine researcher. But this is a widely used molecular biology method I invented, that has great potential to solve our need for a COVID-19 vaccine. Yesterday, I decided to rev up my old computer program “HYDRO” and have a look at COVID-19 to see what I could see. Wow! Was I surprised!

This Hopp and Woods profile for the spike protein of  COVID-19 may not look like much, but great potential lies within it. I’ll get to that in a moment, but first consider this: the genetic sequence of this virus was published just two weeks ago. Since then scientists have been racing to find ways to make a vaccine, but their best estimates are it may take months or even years to come up with a useful product.

But things could be different this time. It turns out my old method easily spotted a key target on COVID-19’s spiky surface where it can be “neutralized.” The image at right shows the amino acid sequence of the spike protein with the short segment my technique zeroed in on shown in red (Peak 1 in the data plot above). According to Hopp and Woods, this is a prime target for making a synthetic peptide vaccine. A what? It’s a type of vaccine that can be made virtually overnight—well, okay, in three days of hard work and late nights in the lab. Can you imagine the tingling up and down my spine as I stared at the computer screen? Here in this humble plot is the blueprint for a vaccine that could save many lives if only I had the lab facilities and chemicals for the task. I’m still getting chills as I write this.

Though I’m retired, there are many labs around the world fully equipped for this sort of vaccine work. I’ve begun making some inquiries, but the wall of corporate secrecy and people unwilling to discuss ongoing projects makes it hard to know if anyone has adopted the idea. Furthermore, there are defective imitations of my computer methods out there, so some labs might end up with sub-par products. Therefore, I’ve decided to lay this out for all to see and let the chips fall where they may. Maybe somewhere someone will pick up this idea and run with it—and wisely so.

I imagined just the sort of pandemic we now face, when I was a grad student at Cornell Medical College in New York City in 1976. I got the idea to use a computer to quickly scan virus sequences and identify the precise spots where antibodies grab on and block the virus’s ability to spread infection. I worked hard and published the method several years later. The Hopp and Woods algorithm is now used by immunochemists around the world to identify “antigenic determinants” that can serve as vaccines. There are now thousands of reports in the literature of immunizations of this type. However, no one ever developed a human vaccine. Admittedly, there’s a reason for that. You see, the immunity to a Hopp and Woods vaccine does not last all that long, only a few months. So the scientific establishment turned up its nose at my method. But tell me folks—right now, would you settle for a few months of immunity to COVID-19? Duh!

I see the dawn of a new day for the technique I pioneered so long ago, precisely because we need a COVID-19 vaccine YESTERDAY. With CDC, NIH, and WHO promising vaccines next fall or next year, how about one we could start testing in just a few days, folks? As the thrill of seeing how well my technique could work wears off, I’m beginning to get a little frustrated. So, let me appeal for help. If you know someone who knows someone who knows someone else who has a vaccine lab, send them my way, all right? Once the necessary chemicals are in hand, we’ll make a vaccine for COVID-19 in three days, or my name ain’t Hopp… of Hopp and Woods. Here’s a link to the original article.

Now, if you’ll bear with me, I’ll explain in more detail just how my method draws a bullseye on the coronavirus. This image zooms in on the molecular interface between the antibody chains (blue for the antibody’s heavy chain, white for its light chain) and again the viral spike protein in red. The interaction has two parts. On the left, the blue heavy chain entangles one part of the viral protein. On the right the light chain surrounds another part. Notice how that right-hand side of the red chain has several Y-shaped things standing up almost like hairs in an electric field? Those are two of the amino acids in the sequence I highlighted in red above. It is precisely this sort of electrostatic interaction that the Hopp and Woods method seeks out. And it seems to have done its job exceedingly well in this case. It has led us directly to the most important target on the whole coronavirus.

In my years of retirement, I haven’t been completely idle. As an exercise in imagination, I wrote a novel that dramatizes an outbreak of a deadly virus and follows scientists as they come up with—you guessed it—a Hopp and Woods vaccine to try and neutralize the threat. The Smallpox Incident was a forum for me to work out the details of just how such a feat might be accomplished. Maybe it should be required reading for vaccinologists responding to the COVID-19 threat, because it breaks the mold of the old vaccine culture that is currently telling us to wait so long.

Given the gravity of the matter at hand—namely life or death by COVID-19—I think it’s time my old method got a second look. So, again, if you know someone with the ways and means to make synthetic peptide vaccines (there are thousands of labs around the world capable of doing this), then send them my way. I’ll help them make it, and then I’ll take the first injection.

This is Part One of a three-part posting about the vaccine. Here are convenient links to:

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They’re fighting coronavirus with a weapon I designed

Posted on February 19, 2020 by Tom Hopp

Coronavirus. Here’s an image of the enemy. As this killer microbe spreads contagion worldwide, it’s heartening to know scientists are already fighting it with a molecular weapon I created a long time ago. Known to medical researchers by the obscure name “FLAG epitope tag,” it’s essentially a molecular handle they can attach to a virus to manipulate it at the atomic level, pulling it apart and putting it together again (in a biohazard containment facility of course) until they understand what makes it tick… and kill.

It turns out that scientists planted my FLAG on the surface of another member of the coronavirus clan, the SARS virus that caused a lethal epidemic in 2003. Attaching it to one of the protein subunits of the virus’s outer shell, they followed the life cycle as it infected human cells in culture flasks, and learned how that protein, ORF3, does its dirty work.


It seems that ORF3 pokes holes in cell membranes, letting water out as the virus compacts itself and takes on a spherical form as it exits one dying cell to find another victim to infect. The yellow highlight I marked on their summary below pinpoints the crucial role my invention played in their ground-breaking discovery.


I only wish I could say that their research has culminated in a cure, but that day has not arrived just yet. But it is surely coming. Now that scientists know ORF3’s function, they can begin to design drugs that target it, perhaps by plugging the holes it pokes in cells. And when that day comes, humanity will benefit immensely from a treatment now lacking. Many thousands of lives will be saved, thanks in part to a molecular tool I developed so long ago. Even though my career has been sidelined, I am heartened and more than a little humbled to see others still carrying on with my invention. Someday, not only the current COVID-19 coronavirus from Wuhan, but all its evil kin, will be annihilated by drugs targeting ORF3. Mankind will then be able to add coronavirus to the list of permanently defeated pathogens. Let’s all hope that day comes soon.

I’m retired now and my lab days are over, but my old heart is warmed by knowledge that others have taken work I started three decades ago in new directions I couldn’t have imagined when I first published the method (here’s a link to the original article).

May the day of coronavirus’s death come soon. And long live the FLAG!

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Of Tidal Waves and Tunnels and Highway 99

Posted on January 26, 2020 by Tom Hopp

Here’s something scary I came across while researching my novel The Great Seattle Earthquake. The city’s brand-spanking-new Highway 99 tunnel, which plunges well below sea level near the south end of the waterfront is virtually without protection from a tsunami. Given that a major tidal wave ripped through this area 1100 years ago and we’re about due for another one, I get just a little worried thinking about it. Don’t you?

The image above shows an overhead view of the southbound lanes of Highway 99 emerging from the tunnel at ground level–and ground level is very close to sea level here, as I have explained before. Have a look at the area from another perspective:


I took this shot standing on a street corner in the waterfront district of Seattle (the spot appears in the first photo in the upper left corner). At first glance, you don’t see much, do you? Just a couple of stadiums in the background. But pay attention to what’s directly ahead if you want to share my heebie-jeebies. That long, low wall is the only protection those emerging lanes have, should a tidal wave come along. It’s about four feet tall judging by the white car just beyond its left end.

That’s it, folks. As I took the shot I was acutely aware that behind me, only about a city block away, was Puget Sound. Next, I took a hike around to get some other perspectives. Nothing I saw inspired confidence. The northbound lanes also drop into a hole in the ground with equivalent protection–that is, nearly none at all.

Here’s a shot of the northbound on ramp, or should I say down ramp? The lucky folks in the SUV passed through the tunnel and went on their way without interference from either earthquake or tidal wave. But look at the city Transit Authority vehicles to the right. They show, again, that the wall is about four feet high. And wait a minute, the spot where I stood to take the photo has no wall at all. The ramp starts right at ground level and is totally unprotected from a wave bigger than an inch or two tall. And tidal waves get A LOT bigger.

Finally, just for the eeriness factor, consider this shot of workers finishing construction of the northbound entrance about a year ago. Imagine an eight- or ten-foot wall of water pouring over the brink of the wall. It would make a thunderous roar comparable to Snoqualmie Falls and it would fill the tunnel far too quickly for anyone on foot, or in a car, to get out.

Maybe it’s time for some city planners to come up with a disaster-preparedness concept here. I’ve got an idea! How about some bigger walls?

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