This diary on the rec list today contained the following assertion:
The way that the Lyme bacteria disperses itself through the body causes a significant immune response that, in some people, continues long after the bacteria are gone. Basically, they get into all kinds of places, and the immune system, on a crusade to drive them out, attacks the body itself. [3] Antibiotics cannot fix that.
[emphasis added]
A little further research would have shown that the highlighted statement, which is the main thesis of the diary, may not be true and in fact may be completely false.
From the wikipedia article on doxycycline:
Experimental applications
At subantimicrobial doses, doxycycline is an inhibitor of matrix metalloproteinases, and has been used in various experimental systems for this purpose; such as for recalcitrant recurrent corneal erosions. Doxycycline has been used successfully in the treatment of one patient with lymphangioleiomyomatosis, an otherwise progressive and fatal disease. Doxycyline has also been shown to attenuate cardiac hypertrophy (in mice), a deadly consequence of prolonged hypertension.
...
Other experimental applications include [excerpted]:
* Rheumatoid arthritis and reactive arthritis.
* Chronic inflammatory lung diseases (panbronchiolitis, asthma, cystic fibrosis, bronchitis)[27][28]
* Prevention of aortic aneurysm in people with Marfan Syndrome. [not just Marfan's related]
* Multiple sclerosis
Matrix metalloprteinases (MMP) are your body's demolition crew. For example, MMP-9 attacks collagen and elastin - it helps with wound healing, and it also plays a significant role in creating wrinkled skin and abdominal aortic aneurysms, by destroying the collagen and elastin that form the extracellular matrix of the artery wall.
What the conditions listed above have in common is that they are all autoimmune, inflammatory diseases - the kind the author asserts can't be fixed by antibiotics. Tetracycline family antibiotics like doxycycline have properties other than as antibiotics or antiparasitics. According to my doctor, doxycycline may also be prophylactic against intestinal cancer.
I have no idea whether doxycycline is effective in treating long-term complications of Lyme disease, but the author's flat-out statement, especially when he's acknowledging an inflammatory or autoimmune response being present, simply is wrong.
My suggestion would be to not take either the author's or wikipedia's word for it, but to do your own research (which I've done for my disease - one on the list above). Simply google any disease above in combination with doxycycline and you should turn up related journal articles. You might even be able to read some of them without a subscription.
There was enough evidence to convince my very cautious family physician to prescribe doxycycline off-label for a immune disorder. She was also smart enough to monitor liver function (not usually listed as a doxycycline side-effect) and I discontinued it when my liver enzymes became elevated.